Anti-ephb2 antibodies and methods using same

ABSTRACT

The invention provides anti-EphB2 antibodies, immunoconjugates, and compositions comprising and methods of using these antibodies and immunoconjugates.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a National Stage of International Application No.PCT/US2006/003502, filed Jan. 31, 2006, which claims the benefit under35 USC §119 to Provisional Application 60/648,541, filed Jan. 31, 2005,and U.S. Provisional Application 60/756,844, filed Jan. 5, 2006, theentire contents of which are hereby incorporated by reference.

FIELD OF THE INVENTION

The present invention relates generally to the fields of molecularbiology. More specifically, the invention concerns anti-EphB2antibodies, and uses of same.

BACKGROUND OF THE INVENTION

The EphB2 receptor (“EphB2” or “EphB2R”) is a member of the eph receptorfamily, which constitutes the largest family of tyrosine kinasereceptors in the human genome (reviewed in Dodelet, Oncogene, 19:5614-5619, 2000). The human eph receptor tyrosine kinases arecategorized by sequence identity into an A class and a B class withcorresponding A-type and B-type ligands referred to as ephrins.Signaling can occur in a forward manner, in which the receptor tyrosinekinase is activated by the ligand, and in a reverse manner, in which thetransmembrane ephrinB ligands are activated by interaction withreceptors. Eph receptor ligand interactions have been implicated in awide range of biological functions including axon guidance, tissueborder formation, vasculogenesis, and cell motility (Kullander et al.Nat. Rev. Mol. Cell. Biol., 3: 475-486, 2002; Cheng et al. CytokineGrowth Factor Rev., 13: 75-85, 2002; Coulthard et al. Int. J. Dev.Biol., 46: 375-384, 2002).

The EphB2 receptor has an extracellular region with a cysteine-richmotif extending over its amino-terminal half followed by two fibronectintype II motifs. There is an intracellular domain featuring a conservedkinase region and a transmembrane domain. EphB2 binds ligands such asephrin-B1, ephrin-B2, and ephrin-B3. The cytoplasmic regions of theactivated EphB2 receptor has been reported to interact with myriadfamiliar signaling molecules such as Src, Grb2, and Abl (Holland et al.,EMBO J., 16: 3877-3888, 1997; Zisch et al., Oncogene, 16: 2657-2670,1998; Yu et al., Oncogene, 20: 3995-4006, 2001). The EphB2 receptortyrosine kinase down-regulates the ras/mitogen-activated protein (MAP)kinase signaling pathway and also inhibits the ab1 tyrosine kinase inendothelial and neuronal cells (Yu et al., Oncogene, 20: 3995-4006,2001; Kim et al., FASEB J., 16: 1126-1128, 2002; Elowe et al. Mol. Cell.Biol., 21: 7429-7441, 2001).

Upregulation of both ephrin ligand and Eph receptor family members hasbeen described in a range of human tumors and cell lines. For instance,EphB2 is reported to be over-expressed in small cell lung cancer (Tanget al., Clin Cancer Res 1999; 5:455-60), neuroblastomas, (Tang et al.,Med Pediatr Oncol 2001; 36:80-2), melanoma (Vogt et al. Clin Cancer Res1998; 4:791-7), breast carcinoma (Wu et al., Pathol Oncol Res 2004;10:26-33), colorectal cancer (CRC) (Jubb et al., co-owned, co-pendingU.S. patent application No. 60/642,164, filed Jan. 6, 2005, and Cairnset al., WO2003/000113) and hepatocellular carcinoma (Hafner et al., ClinChem 2004; 50:490-9).

Antibody-based therapy has proved very effective in the treatment ofvarious disorders. For example, HERCEPTIN™ and RITUXAN™ (both fromGenentech, S. San Francisco), have been used successfully to treatbreast cancer and non-Hodgkin's lymphoma, respectively. HERCEPTIN™ is arecombinant DNA-derived humanized monoclonal antibody that selectivelybinds to the extracellular domain of the human epidermal growth factorreceptor 2 (HER2) proto-oncogene. HER2 protein overexpression isobserved in 25-30% of primary breast cancers. RITUXAN™ is a geneticallyengineered chimeric murine/human monoclonal antibody directed againstthe CD20 antigen found on the surface of normal and malignant Blymphocytes. Both these antibodies are produced in CHO cells.

The use of antibody-drug conjugates (ADC), i.e. immunoconjugates, forthe local delivery of agents such as cytotoxic or cytostatic agents tokill or inhibit tumor cells in the treatment of cancer (Syrigos andEpenetos (1999) Anticancer Research 19:605-614; Niculescu-Duvaz andSpringer (1997) Adv. Drug Del. Rev. 26:151-172; U.S. Pat. No. 4,975,278)allows targeted delivery of the drug moiety to tumors, and intracellularaccumulation therein, where systemic administration of theseunconjugated drug agents may result in unacceptable levels of toxicityto normal cells as well as the tumor cells sought to be eliminated(Baldwin et al (1986) Lancet pp. (Mar. 15, 1986):603-05; Thorpe, (1985)“Antibody Carriers Of Cytotoxic Agents In Cancer Therapy: A Review,” inMonoclonal Antibodies '84: Biological And Clinical Applications, A.Pinchera et al (eds), pp. 475-506).

It is clear that there continues to be a need for agents that haveclinical attributes that are optimal for development as therapeuticagents. The invention described herein meets this need and providesother benefits.

All references cited herein, including patent applications andpublications, are incorporated by reference in their entirety.

SUMMARY OF THE INVENTION

The invention is in part based on the identification of a variety ofEphB2 binding agents (such as immunoconjugates, antibodies, andfragments thereof). EphB2 presents as an important and advantageoustherapeutic target, and the invention provides compositions and methodsbased on binding EphB2. EphB2 binding agents of the invention, asdescribed herein, provide important therapeutic and diagnostic agentsfor use in targeting pathological conditions associated with expressionand/or activity of the EphB2-EphB2 ligand pathways. Accordingly, theinvention provides methods, compositions, kits and articles ofmanufacture related to EphB2 binding.

The present invention provides antibodies that bind to EphB2.

In one aspect, the invention provides the antibody produced by hybridomacell line 2H9.11.14 having American Tissue Type Culture (ATCC) No.PTA-6606, deposited on Feb. 24, 2005.

In one aspect, the invention provides an isolated antibody comprisingheavy and/or light chain variable domain(s) of the antibody produced byhybridoma cell line 2H9.11.14 having American Tissue Type Culture (ATCC)No. PTA-6606, wherein said isolated antibody specifically binds humanEphB2.

In one aspect, the invention provides an isolated antibody comprising atleast one (at least 2, at least 3, at least 4, at least 5, and/or 6)hypervariable sequence(s) (HVR(s)) comprising a sequence selected fromthe group consisting of HVR-L1, HVR-L2, HVR-L3, HVR-H1, HVR-H2, and/orHVR-H3 of the antibody produced by hybridoma cell line 2H9.11.14 havingAmerican Tissue Type Culture (ATCC) No. PTA-6606, wherein said isolatedantibody specifically binds human EphB2.

In one aspect, the invention provides an isolated antibody that binds tothe same epitope on human EphB2 as the antibody produced by hybridomacell line 2H9.11.14 having American Tissue Type Culture (ATCC) No.PTA-6606.

In one aspect, the invention provides an isolated antibody that competeswith the antibody produced by hybridoma cell line 2H9.11.14 havingAmerican Tissue Type Culture (ATCC) No. PTA-6606 for binding to humanEphB2.

In one aspect, the invention provides an isolated anti-EphB2 antibody,wherein a full length IgG form of the antibody specifically binds humanEphB2 with a binding affinity of 70 pM or better. As is well-establishedin the art, binding affinity of a ligand to its receptor can bedetermined using any of a variety of assays, and expressed in terms of avariety of quantitative values. Accordingly, in one embodiment, thebinding affinity is expressed as Kd values and reflects intrinsicbinding affinity (e.g., with minimized avidity effects). Generally andpreferably, binding affinity is measured in vitro, whether in acell-free or cell-associated setting. Any of a number of assays known inthe art, including those described herein, can be used to obtain bindingaffinity measurements, including, for example, Biacore, radioimmunoassay(RIA) and ELISA.

In one aspect, the invention provides an isolated antibody that binds aligand binding region of EphB2. In some embodiments, the isolatedantibody binds a polypeptide comprising, consisting of or consistingessentially of amino acids about 19 to about 208 of human EphB2 (FIG.12).

In one aspect, the invention provides an isolated anti-EphB2 antibodythat competes with EphB2 ligand for binding of EphB2.

In one aspect, the invention provides an isolated anti-EphB2 antibodythat inhibits, reduces, and/or blocks EphB2 activity. In someembodiments, EphB2 autophosphorylation is inhibited, reduced, and/orblocked.

In one aspect, the invention provides an anti-EphB2 antibody comprising:at least one, two, three, four, five, and/or six hypervariable region(HVR) sequences selected from the group consisting of: (a) HVR-L1comprising sequence KSSQSLLNSGNQENYLA (SEQ ID NO: 1); (b) HVR-L2comprising sequence GASTRES (SEQ ID NO:2); (c) HVR-L3 comprisingsequence QNDHSYPFT (SEQ ID NO:3); (d) HVR-H1 comprising sequence SYWMH(SEQ ID NO:4); (e) HVR-H2 comprising sequence FINPSTGYTDYNQKFKD (SEQ IDNO:5); and (f) HVR-H3 comprising sequence RLKLLRYAMDY (SEQ ID NO:6).

In one embodiment, an antibody of the invention comprises a light chaincomprising at least one, at least two or all three of HVR sequencesselected from the group consisting of KS SQSLLNSGNQENYLA (SEQ ID NO: 1),GASTRES (SEQ ID NO:2), and QNDHSYPFT (SEQ ID NO:3). In one embodiment,the antibody comprises light chain HVR-L1 having amino acid sequenceKSSQSLLNSGNQENYLA (SEQ ID NO:1). In one embodiment, the antibodycomprises light chain HVR-L2 having amino acid sequence GASTRES (SEQ IDNO:2). In one embodiment, the antibody comprises light chain HVR-L3having amino acid sequence QNDHSYPFT (SEQ ID NO:3). In one embodiment,an antibody of the invention comprises a heavy chain comprising at leastone, at least two or all three of HVR sequences selected from the groupconsisting of SYWMH (SEQ ID NO:4), FINPSTGYTDYNQKFKD (SEQ ID NO:5), andRLKLLRYAMDY (SEQ ID NO:6). In one embodiment, the antibody comprisesheavy chain HVR-H1 having amino acid sequence SYWMH (SEQ ID NO:4). Inone embodiment, the antibody comprises heavy chain HVR-H2 having aminoacid sequence FINPSTGYTDYNQKFKD (SEQ ID NO:5). In one embodiment, theantibody comprises heavy chain HVR-H3 having amino acid sequenceRLKLLRYAMDY (SEQ ID NO:6). In one embodiment, an antibody of theinvention comprises a heavy chain comprising at least one, at least twoor all three of HVR sequences selected from the group consisting ofSYWMH (SEQ ID NO:4), FINPSTGYTDYNQKFKD (SEQ ID NO: 5), and RLKLLRYAMDY(SEQ ID NO: 6) and a light chain comprising at least one, at least twoor all three of HVR sequences selected from the group consisting ofKSSQSLLNSGNQENYLA (SEQ ID NO:1), GASTRES (SEQ ID NO:2), and QNDHSYPFT(SEQ ID NO:3).

In one embodiment, an antibody of the invention comprises a light chainvariable domain having the sequence:

(SEQ ID NO:7) DIVMTQSPSSLSVSAGEKVTMNCKSSQSLLNSGNQENYLAWYQQKPGQPPKLLIYGASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCQNDHSY PFTFGAGTKVEIKR.

In one embodiment, an antibody of the invention comprises a heavy chainvariable domain having the sequence:

(SEQ ID NO:8) QVQLQQSGAELAKPGASVKMSCKASGYTFTSYWMHWVKQRPGQGLEWIGFINPSTGYTDYNQKFKDKATLTVKSSNTAYMQLSRLTSEDSAVYYCTRRLK LLRYAMDYWGQGTTLTVSA.

In one embodiment, an antibody of the invention comprises a light chainvariable domain having the sequence:

DIVMTQSPSSLSVSAGEKVTMNCKSSQSLLNSGNQENYLAWYQQKPGQPPKLLIYGASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCQNDHSYPFTFGAGTKVEIKR (SEQ ID NO:7); andcomprises a heavy chain variable domain having the sequence:

(SEQ ID NO:8) QVQLQQSGAELAKPGASVKMSCKASGYTFTSYWMHWVKQRPGQGLEWIGFINPSTGYTDYNQKFKDKATLTVKSSNTAYMQLSRLTSEDSAVYYCTRRLK LLRYAMDYWGQGTTLTVSA.

In one aspect, the invention provides an antibody that competes with anyof the above-mentioned antibodies for binding to EphB2. In one aspect,the invention provides an antibody that binds to the same epitope onEphB2 as any of the above-mentioned antibodies.

As is known in the art, and as described in greater detail hereinbelow,the amino acid position/boundary delineating a hypervariable region ofan antibody can vary, depending on the context and the variousdefinitions known in the art (as described below). Some positions withina variable domain may be viewed as hybrid hypervariable positions inthat these positions can be deemed to be within a hypervariable regionunder one set of criteria while being deemed to be outside ahypervariable region under a different set of criteria. One or more ofthese positions can also be found in extended hypervariable regions (asfurther defined below).

In some embodiments, the antibody is a monoclonal antibody. In someembodiments, the antibody is a polyclonal antibody. In some embodiments,the antibody is selected from the group consisting of a chimericantibody, an affinity matured antibody, a humanized antibody, and ahuman antibody. In some embodiments, the antibody is an antibodyfragment. In some embodiments, the antibody is a Fab, Fab′, Fab′-SH,F(ab′)₂, or scFv.

In one embodiment, the antibody is a chimeric antibody, for example, anantibody comprising antigen binding sequences from a non-human donorgrafted to a heterologous non-human, human or humanized sequence (e.g.,framework and/or constant domain sequences). In one embodiment, thenon-human donor is a mouse. In one embodiment, an antigen bindingsequence is synthetic, e.g. obtained by mutagenesis (e.g., phage displayscreening, etc.). In one embodiment, a chimeric antibody of theinvention has murine V regions and human C region. In one embodiment,the murine light chain V region is fused to a human kappa light chain.In one embodiment, the murine heavy chain V region is fused to a humanIgG1 C region.

Humanized antibodies of the invention include those that have amino acidsubstitutions in the FR and affinity maturation variants with changes inthe grafted CDRs. The substituted amino acids in the CDR or FR are notlimited to those present in the donor or recipient antibody. In otherembodiments, the antibodies of the invention further comprise changes inamino acid residues in the Fc region that lead to improved effectorfunction including enhanced CDC and/or ADCC function and B-cell killing.Other antibodies of the invention include those having specific changesthat improve stability. Antibodies of the invention also include fucosedeficient variants having improved ADCC function in vivo. In otherembodiments, the antibodies of the invention comprise changes in aminoacid residues in the Fc region that lead to decreased effector function,e.g. decreased CDC and/or ADCC function and/or decreased B-cell killing.In some embodiments, the antibodies of the invention are characterizedby decreased binding (such as absence of binding) to human complementfactor C1q and/or human Fc receptor on natural killer (NK) cells. Insome embodiments, the antibodies of the invention are characterized bydecreased binding (such as the absence of binding) to human FcγRI,FcγRIIA, and/or FcγRIIIA. In some embodiments, the antibodies of theinvention is of the IgG class (e.g., IgG1 or IgG4) and comprises atleast one mutation in E233, L234, L235, G236, D265, D270, N297, E318,K320, K322, A327, A330, P331 and/or P329 (numbering according to the EUindex). In some embodiments, the antibodies comprise the mutationL234A/L235A or D265A/N297A.

In one aspect, the invention provides anti-EphB2 polypeptides comprisingany of the antigen binding sequences provided herein, wherein theanti-EphB2 polypeptides specifically bind to EphB2.

In one aspect, the invention provides an immunoconjugate(interchangeably termed “antibody drug conjugate” or “ADC”) comprisingany of the anti-EphB2 antibodies disclosed herein conjugated to anagent, such as a drug. EphB2 overexpression has been observed in gastriccancer, small cell lung cancer, neuroblastomas, melanoma, breastcarcinoma, and hepatocellular carcinoma and in all stages of colorectaltumorogenesis, indicating that EphB2 is a suitable target forimmunoconjugate therapy. EphB2 expression has been observed in colonadenomas, indicating that EphB2 is a suitable target for disorderscharacterized by colon adenomas.

In some embodiments, the drug in the immunoconjugate is achemotherapeutic agent, a growth inhibitory agent, a toxin (e.g., anenzymatically active toxin of bacterial, fungal, plant, or animalorigin, or fragments thereof), or a radioactive isotope (i.e., aradioconjugate). In some embodiments, the drug is a maytansinoid, anauristatin, a dolastatin, or a calicheamicin. In some embodiments, thedrug is DM1, DM3, DM4, MMAE, or MMAF.

In the immunoconjugates of the invention, an antibody (Ab) is conjugatedto one or more drug moieties (D), e.g. about 1 to about 20 drug moietiesper antibody, through a linker (L). In some embodiments, the linkercomprises linker components selected from one or more of6-maleimidocaproyl (“MC”), maleimidopropanoyl (“MP”), valine-citrulline(“val-cit”), alanine-phenylalanine (“ala-phe”), p-aminobenzyloxycarbonyl(“PAB”), N-Succinimidyl 4-(2-pyridylthio) pentanoate (“SPP”),N-Succinimidyl 4-(N-maleimidomethyl)cyclohexane-1 carboxylate (“SMCC”),and/or N-Succinimidyl (4-iodo-acetyl) aminobenzoate (“SIAB”). In someembodiments, the linker comprises MC-val-cit-PAB.

In some embodiments, the immunoconjugate comprises SPP-DM1, SMCC-DM1,BMPEO-DM1, MC-vc-PAB-MMAF, MC-vc-PAB-MMAE, MC-MMAF, or MC-MMAE.

In one aspect, the invention provides an immunoconjugate comprising ananti-EphB2 antibody that kills tumor cells. In some embodiments, tumorcells are killed in vitro (in some embodiments, with an IC50 of about 50ng/ml, 40 ng/ml, 30 ng/ml, 20 ng/ml, 10 ng/ml, 5 ng/ml, 1 ng/ml, orless, such as 900 pg/ml, 800 pg/ml, 700 pg/ml, 600 pg/ml, 500 pg/ml, orless). In some embodiments, tumor cells are killed in vivo. In someembodiments, administration of the immunoconjugate reduces tumor growth(in some embodiments, having about 90%, 80%, 70%, 60%, 50%, 40%, 30%,20% or 10%, or less reduction in tumor growth compared to a controltumor) or reduces time to tumor doubling.

The antibodies and immunoconjugates of the invention bind (such asspecifically bind) EphB2, and in some embodiments, may modulate one ormore aspects of EphB2-associated effects, including but not limited toEphB2 activation, EphB2 downstream molecular signaling, EphB2 ligandactivation, EphB2 ligand downstream molecular signaling, disruption ofligand (e.g., ephrin-B1, ephrin-B2, and/or ephrin-B3) binding to EphB2,EphB2 phosphorylation and/or EphB2 multimerization, and/or EphB2 ligandphosphorylation, and/or disruption of any biologically relevant EphB2and/or EphB2 ligand biological pathway, and/or treatment and/orprevention of a tumor, cell proliferative disorder or a cancer; and/ortreatment or prevention of a disorder associated with EphB2 expressionand/or activity (such as increased EphB2 expression and/or activity). Insome embodiments, the antibody or immunoconjugate of the inventionspecifically binds to EphB2. In some embodiments, the antibody orimmunoconjugate specifically binds to the EphB2 extracellular domain(ECD). In some embodiments, the antibody or immunoconjugate specificallybinds to a polypeptide consisting of or consisting essentially of aminoacids about 19 to about 208 of human EphB2. In some embodiments, theantibody or immunoconjugate specifically binds EphB2 with a KD of 70 pMor stronger. In some embodiments, the antibody or immunoconjugate of theinvention reduces, inhibits, and/or blocks EphB2 activity in vivo and/orin vitro. In some embodiments, the antibody or immunoconjugate reduces,inhibits and/or blocks EphB2 autophosphorylation. In some embodiments,the antibody or immunoconjugate competes for binding with EphB2-ligand(reduces and/or blocks EphB2 ligand binding to EphB2). In someembodiments, the antibody or immunoconjugate is internalized uponbinding to EphB2 expressed on a mammalian cell.

In one aspect, the invention provides use of an antibody orimmunoconjugate of the invention in the preparation of a medicament forthe therapeutic and/or prophylactic treatment of a disorder, such as acancer, a tumor, and/or a cell proliferative disorder. In someembodiments, the disorder is characterized by colon adenomas.

In one aspect, the invention provides compositions comprising one ormore antibodies or immunoconjugates of the invention and a carrier. Inone embodiment, the carrier is pharmaceutically acceptable.

In one aspect, the invention provides nucleic acids encoding ananti-EphB2 antibody of the invention.

In one aspect, the invention provides vectors comprising a nucleic acidof the invention.

In one aspect, the invention provides compositions comprising one ormore nucleic acid of the invention and a carrier. In one embodiment, thecarrier is pharmaceutically acceptable.

In one aspect, the invention provides host cells comprising a nucleicacid or a vector of the invention. A vector can be of any type, forexample a recombinant vector such as an expression vector. Any of avariety of host cells can be used. In one embodiment, a host cell is aprokaryotic cell, for example, E. coli. In one embodiment, a host cellis a eukaryotic cell, for example a mammalian cell such as ChineseHamster Ovary (CHO) cell.

In one aspect, the invention provides methods of making an antibody orimmunoconjugate of the invention. For example, the invention providesmethods of making an anti-EphB2 antibody (which, as defined hereinincludes full length and fragments thereof) or immunoconjugate, saidmethod comprising expressing in a suitable host cell a recombinantvector of the invention encoding said antibody (or fragment thereof),and recovering said antibody. The invention further provides methods ofmaking an anti-EphB2 immunoconjugate, said method comprising expressingin a suitable host cell a recombinant vector of the invention encodingan anti-EphB2 antibody (or fragment thereof) or the invention,recovering said anti-EphB2 antibody, and conjugating the anti-EphB2antibody to a drug.

In one aspect, the invention provides an article of manufacturecomprising a container; and a composition contained within thecontainer, wherein the composition comprises one or more anti-EphB2antibodies or immunoconjugates of the invention. In one embodiment, thecomposition comprises a nucleic acid of the invention. In oneembodiment, a composition comprising an antibody or immunoconjugatefurther comprises a carrier, which in some embodiments ispharmaceutically acceptable. In one embodiment, an article ofmanufacture of the invention further comprises instructions foradministering the composition (for e.g., the antibody) to a subject(such as instructions for any of the methods described herein).

In one aspect, the invention provides a kit comprising a first containercomprising a composition comprising one or more anti-EphB2 antibodies orimmunoconjugates of the invention; and a second container comprising abuffer. In one embodiment, the buffer is pharmaceutically acceptable. Inone embodiment, a composition comprising an antibody or immunoconjugatefurther comprises a carrier, which in some embodiments ispharmaceutically acceptable. In one embodiment, a kit further comprisesinstructions for administering the composition (for e.g., the antibody)to a subject.

In one aspect, the invention provides use of an anti-EphB2 antibody orimmunoconjugate (in some embodiments, an anti-EphB2 antibody orimmunoconjugate of the invention) in the preparation of a medicament forthe therapeutic and/or prophylactic treatment of a disorder, such as acancer, a tumor, and/or a cell proliferative disorder.

In one aspect, the invention provides use of a nucleic acid of theinvention in the preparation of a medicament for the therapeutic and/orprophylactic treatment of a disorder, such as a cancer, a tumor, and/ora cell proliferative disorder.

In one aspect, the invention provides use of an expression vector of theinvention in the preparation of a medicament for the therapeutic and/orprophylactic treatment of a disorder, such as a cancer, a tumor, and/ora cell proliferative disorder.

In one aspect, the invention provides use of a host cell of theinvention in the preparation of a medicament for the therapeutic and/orprophylactic treatment of a disorder, such as a cancer, a tumor, and/ora cell proliferative disorder.

In one aspect, the invention provides use of an article of manufactureof the invention in the preparation of a medicament for the therapeuticand/or prophylactic treatment of a disorder, such as a cancer, a tumor,and/or a cell proliferative disorder.

In one aspect, the invention provides use of a kit of the invention inthe preparation of a medicament for the therapeutic and/or prophylactictreatment of a disorder, such as a cancer, a tumor, and/or a cellproliferative disorder.

The invention provides methods and compositions useful for modulatingdisease states associated with expression and/or activity of EphB2, suchas increased expression and/or activity or undesired expression and/oractivity or decreased expression and/or activity.

In one aspect, the invention provides methods for treating or preventinga tumor, a cancer, and/or a cell proliferative disorder associated withincreased expression and/or activity of EphB2, the methods comprisingadministering an effective amount of an anti-EphB2 antibody orimmunoconjugate (in some embodiments, an anti-EphB2 antibody of theinvention) to a subject in need of such treatment.

In one aspect, the invention provides methods for killing a cell (suchas a cancer or tumor cell), the methods comprising administering aneffective amount of an anti-EphB2 antibody or immunoconjugate (in someembodiments, an anti-EphB2 antibody of the invention) to a subject inneed of such treatment.

In one aspect, the invention provides methods for reducing, inhibiting,blocking, or preventing growth of a tumor or cancer, the methodscomprising administering an effective amount of an anti-EphB2 antibodyor immunoconjugate (in some embodiments, an anti-EphB2 antibody of theinvention) to a subject in need of such treatment.

In one aspect, the invention provides methods for treating or preventinga neuropathy or neurodegenerative disease, or repairing a damaged nervecell, the methods comprising administering an effective amount of ananti-EphB2 antibody or immunoconjugate (in some embodiments, ananti-EphB2 antibody of the invention) to a subject in need of suchtreatment.

In one aspect, the invention provides methods for promoting thedevelopment, proliferation, maintenance or regeneration of neurons, themethods comprising administering an effective amount of an anti-EphB2antibody or immunoconjugate (in some embodiments, an anti-EphB2 antibodyof the invention) to a subject in need of such treatment.

In one aspect, the invention provides methods for inhibitingangiogenesis, the methods comprising administering an effective amountof an anti-EphB2 antibody or immunoconjugate (in some embodiments, ananti-EphB2 antibody of the invention) to a subject in need of suchtreatment. In some embodiments, the site of angiogenesis is a tumor orcancer.

Methods of the invention can be used to affect any suitable pathologicalstate. Exemplary disorders are described herein, and include a cancerselected from the group consisting of small cell lung cancer,neuroblastomas, melanoma, breast carcinoma, gastric cancer, colorectalcancer (CRC), and hepatocellular carcinoma; and disorders characterizedby colon adenomas.

In one embodiment, a cell that is targeted in a method of the inventionis a cancer cell. For example, a cancer cell can be one selected fromthe group consisting of a breast cancer cell, a colorectal cancer cell,a lung cancer cell, a papillary carcinoma cell, a colon cancer cell, apancreatic cancer cell, an ovarian cancer cell, a cervical cancer cell,a central nervous system cancer cell, an osteogenic sarcoma cell, arenal carcinoma cell, a hepatocellular carcinoma cell, a bladder cancercell, a gastric carcinoma cell, a head and neck squamous carcinoma cell,a melanoma cell, a leukemia cell, and a colon adenoma cell. In oneembodiment, a cell that is targeted in a method of the invention is ahyperproliferative and/or hyperplastic cell. In one embodiment, a cellthat is targeted in a method of the invention is a dysplastic cell. Inyet another embodiment, a cell that is targeted in a method of theinvention is a metastatic cell. In some embodiments, the cell that istargeted is a colon adenoma cell. In some embodiments, the cell that istargeted expresses on the cell membrane at least about 20,000; 30,000;40,000; 50,000; 60,000; 70,000; 80,000; 90,000; 100,000; 150,000;200,000; 250,000; 300,000; 350,000; 400,000; 450,000; 500,000; 550,000;600,000; 650,000; 700,000; 750,000; 800,000; 850,000, or more EphB2molecules.

Methods of the invention can further comprise additional treatmentsteps. For example, in one embodiment, a method further comprises a stepwherein a targeted cell and/or tissue (for e.g., a cancer cell) isexposed to radiation treatment or a chemotherapeutic agent.

In another aspect, the invention provides methods for detection ofEphB2, the methods comprising detecting EphB2-anti-EphB2 antibodycomplex in the sample. The term “detection” as used herein includesqualitative and/or quantitative detection (e.g., measuring levels) withor without reference to a control.

In another aspect, the invention provides methods for diagnosing adisorder associated with EphB2 expression and/or activity, the methodscomprising detecting EphB2-anti-EphB2 antibody complex in a biologicalsample from a patient having or suspected of having the disorder. Insome embodiments, the EphB2 expression is increased expression orabnormal expression. In some embodiments, the disorder is a tumor,cancer, and/or a cell proliferative disorder.

In another aspect, the invention provides any of the anti-EphB2antibodies described herein, wherein the anti-EphB2 antibody comprises adetectable label.

In another aspect, the invention provides a complex of any of theanti-EphB2 antibodies described herein and EphB2. In some embodiments,the complex is in vivo or in vitro. In some embodiments, the complexcomprises a cancer cell. In some embodiments, the anti-EphB2 antibody isdetectably labeled.

In another aspect, the invention provides a polypeptide comprising,consisting of, or consisting essentially of amino acids 19-208 of EphB2(FIG. 12).

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1: depicts the amino acid sequences of monoclonal antibody 2H9heavy chain variable region. Amino acids are numbered according toKabat.

FIG. 2: depicts the amino acid sequence of monoclonal antibody 2H9 lightchain variable regions. Amino acids are numbered according to Kabat.

FIG. 3: EphB2 mRNA is overexpressed in human cancer tissues versesnormal human tissues. A, oligonucleotide microarray analysis wasperformed on RNA extracted from 38 human colorectal tumors and 7specimens of normal human colonic mucosa. The average differencerepresents signal intensity (scaled to 1500). B, real-time PCR wasperformed on RNA extracted from 11 human colorectal cancer biopsyspecimens and the corresponding patient-matched normal colon tissuespecimens.

FIG. 4: EphB2 expression in cancer and normal human colon tissues. A, insitu hybridization. EphB2 transcript is detected as deposited silvergrains in the dark-field images, and the corresponding bright-fieldimages were generated by staining the sections with H&E. Top and bottompanels are from colon tumor and normal colon tissues, respectively. B,EphB2 protein expression was detected using immunohistochemistry. Frozenserial tissue sections of a human adenocarcinoma were stained withanti-EphB2 monoclonal antibody 2H9 (right panel) or with controlantibody (left panel) and counterstained with hematoxylin.

FIG. 5: Monoclonal antibody (MAb) 2H9 antagonizes the ephrin-EphB2interaction. A, the SVT2-EphB2 cell line was incubated with purifiedFc-EphrinB2 fusion protein, and EphB2 protein was recovered from celllysates by immunoprecipitation (IP) through the GD epitope tag fused toits NH2 terminus. Western blotting (WB) was performed withanti-phosphotyrosine (PTyr; top panel), to detect phosphotyrosine, andanti-GD (bottom panel), to detect total EphB2 protein. During ligandincubation, MAb 2H9 or control antibody (EGVEGF MAb) was included in theculture medium. B, binding of purified human Fc-EphrinB1 fusion proteinto HT1080 cells overexpressing EphB2 was assessed by flow cytometryusing human anti-Fc conjugated to FITC. Relative fluorescence intensitywas then measured in the presence of increasing concentrations of MAb2H9. As controls, Fc-EphrinB1 was omitted in the presence or absence ofMab 2H9 or secondary antibody.

FIG. 6: Internalization of anti-EphB2 monoclonal antibody (Mab) 2H9. A,MAb 2H9 was incubated on ice with HT1080 cells overexpressing EphB2. Thecells either remained on ice or were shifted to 37° C. for 1 h beforefixing and staining with secondary antibody. B, Mab 2H9 was labeled with¹²⁵I and incubated with HT1080-EphB2 cells on ice. Cells remained on ice(4° C.) or were shifted to 37° C. for 1 hour, and then the percentage ofinternalized ¹²⁵I was determined by scintillation counting.

FIG. 7: Immunoconjugate 2H9-MC-valine-citrulline(vc)-PAB-monomethylauristatin E (MMAE) kills tumor cells in vitro. TheHT1080 cell line stably overexpressing EphB2 (HT1080-EphB2) or a vectorcontrol HT1080 cell line (HT1080-GD) was treated with increasingconcentrations of naked (i.e. not conjugated) monoclonal antibody 2H9,immunoconjugate 2H9-MC-vc-PAB-MMAE (abbreviated “MMAE-vc-2H9” in thisfigure), or immunoconjugate anti-interleukin-8-MC-vc-PAB-MMAE(abbreviated “MMAE-vc-anti-IL8” in this figure), and cell viability wasmeasured after 2 days. The antibody concentration required to attainhalf-maximal killing is indicated as IC50.

FIG. 8: Characterization of HT1080 cell lines and immunoconjugate2H9-MC-vc-PAB-MMAE. A, monoclonal antibody 2H9 binding assays wereperformed on the HT1080-EphB2 and HT1080-GD cell lines. The estimatednumber of total binding sites and the dissociation constants (Kd) weredetermined by Scatchard analysis. B, flow cytometry was performed withMAb 2H9 on the HT1080-EphB2 and HT1080-GD cell lines. Relativefluorescence intensity is presented in the histogram for MAb 2H9 and forsecondary antibody only (control). C, saturation binding was performedon the HT1080-EphB2 and HT1080-GD cell lines with both naked Mab 2H9(abbreviated “2H9” in this figure) and immunoconjugate2H9-MC-vc-PAB-MMAE (abbreviated “2H9-vc-MMAE” in this figure). Relativebinding was determined using a horseradish peroxidase-conjugatedsecondary antibody, and absorbance was read at 450 nm.

FIG. 9: Immunoconjugates 2H9-SPP-Dm1, 2H9-SMCC-DM1, 2H9-MC-vc-PAB-MMAE,and 2H9-MC-vc-PAB-MMAF kill tumor cells in vitro. A, the HT1080 cellline stably overexpressing EphB2 (HT1080-EphB2) was treated withincreasing concentrations of 2H9-MC-vc-PAB-MMAE (abbreviated “vc-MMAE”in this figure), 2H9-SMCC-DM1 (abbreviated “SMCC-DM1” in this figure),2H9-SPP-DM1 (abbreviated “Spp-DM1” in this figure), oranti-interleukin-8-MC-vc-PAB-MMAE (abbreviated “IL8MMAE” in thisfigure), and cell viability was measured after 2 days. B, the HT1080cell line stably overexpressing EphB2 (HT1080-EphB2) was treated withincreasing concentrations of 2H9-MC-vc-PAB-MMAE (abbreviated “vc-MMAE”in this figure), 2H9-MC-vc-PAB-MMAF (abbreviated “vc-MMAF” in thisfigure), 2H9-SMCC-DM1 (abbreviated “SMCC-DM1” in this figure), or2H9-SPP-DM1 (abbreviated “Spp-DM1” in this figure), and cell viabilitywas measured after 2 days.

FIG. 10: 2H9-MC-vc-PAB-MMAE specifically inhibits growth of human tumorsin vivo. A, nude mice were inoculated s.c. on one flank with HT1080-GDcells and on the other with HT1080-EphB2, and the resulting tumorxenografts were grown to an average size of 150 mm each. Ten animals ineach group received vehicle control () or 3 mg/kg body weight of eitherimmunoconjugate 2H9 MC-vc-PAB-MMAE (▪) (abbreviated “MMAE-vc-2H9” inthis figure) or immunoconjugate anti-interleukin 8 MC-vc-PAB-MMAE (▴)(abbreviated “MMAE-vc-anti-Il-8” in this figure) once per week. B, theCXF1103 human colon tumor line was grown as a xenograft in nude micethat underwent a treatment protocol identical to that described for theHT1080 model. The control antibody was anti-GD conjugated toMC-vc-PAB-MMAE (abbreviated “MMAE-vc-GD” in this figure). Mean tumorvolumes with SEs are presented.

FIG. 11: depicts an amino acid sequence of the ligand binding domain ofEphB2 (SEQ ID NO:9).

DETAILED DESCRIPTION OF THE INVENTION

The invention herein provides anti-EphB2 antibodies, or immunoconjugatescomprising anti-EphB2 antibodies, that are useful for, e.g., treatmentor prevention of disease states associated with expression and/oractivity of EphB2, such as increased expression and/or activity orundesired expression and/or activity. In some embodiments, theantibodies or immunoconjugates of the invention are used to treat atumor, a cancer, and/or a cell proliferative disorder.

In another aspect, the anti-EphB2 antibodies of the invention findutility as reagents for detection and/or isolation of EphB2, such asdetention of EphB2 in various tissues and cell type.

The invention further provides methods of making anti-EphB2 antibodies,and polynucleotides encoding anti-EphB2 antibodies.

General Techniques

The techniques and procedures described or referenced herein aregenerally well understood and commonly employed using conventionalmethodology by those skilled in the art, such as, for example, thewidely utilized methodologies described in Sambrook et al., MolecularCloning: A Laboratory Manual 3rd. edition (2001) Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y. CURRENT PROTOCOLS INMOLECULAR BIOLOGY (F. M. Ausubel, et al. eds., (2003)); the seriesMETHODS IN ENZYMOLOGY (Academic Press, Inc.): PCR 2: A PRACTICALAPPROACH (M. J. MacPherson, B. D. Hames and G. R. Taylor eds. (1995)),Harlow and Lane, eds. (1988) ANTIBODIES, A LABORATORY MANUAL, and ANIMALCELL CULTURE (R. I. Freshney, ed. (1987)).

DEFINITIONS

An “isolated” antibody is one which has been identified and separatedand/or recovered from a component of its natural environment.Contaminant components of its natural environment are materials whichwould interfere with diagnostic or therapeutic uses for the antibody,and may include enzymes, hormones, and other proteinaceous ornonproteinaceous solutes. In preferred embodiments, the antibody will bepurified (1) to greater than 95% by weight of antibody as determined bythe Lowry method, and most preferably more than 99% by weight, (2) to adegree sufficient to obtain at least 15 residues of N-terminal orinternal amino acid sequence by use of a spinning cup sequenator, or (3)to homogeneity by SDS-PAGE under reducing or nonreducing conditionsusing Coomassie blue or, preferably, silver stain. Isolated antibodyincludes the antibody in situ within recombinant cells since at leastone component of the antibody's natural environment will not be present.Ordinarily, however, isolated antibody will be prepared by at least onepurification step.

An “isolated” nucleic acid molecule is a nucleic acid molecule that isidentified and separated from at least one contaminant nucleic acidmolecule with which it is ordinarily associated in the natural source ofthe antibody nucleic acid. An isolated nucleic acid molecule is otherthan in the form or setting in which it is found in nature. Isolatednucleic acid molecules therefore are distinguished from the nucleic acidmolecule as it exists in natural cells. However, an isolated nucleicacid molecule includes a nucleic acid molecule contained in cells thatordinarily express the antibody where, for example, the nucleic acidmolecule is in a chromosomal location different from that of naturalcells.

The term “variable domain residue numbering as in Kabat” or “amino acidposition numbering as in Kabat”, and variations thereof, refers to thenumbering system used for heavy chain variable domains or light chainvariable domains of the compilation of antibodies in Kabat et al.,Sequences of Proteins of Immunological Interest, 5th Ed. Public HealthService, National Institutes of Health, Bethesda, Md. (1991). Using thisnumbering system, the actual linear amino acid sequence may containfewer or additional amino acids corresponding to a shortening of, orinsertion into, a FR or CDR of the variable domain. For example, a heavychain variable domain may include a single amino acid insert (residue52a according to Kabat) after residue 52 of H2 and inserted residues(e.g. residues 82a, 82b, and 82c, etc according to Kabat) after heavychain FR residue 82. The Kabat numbering of residues may be determinedfor a given antibody by alignment at regions of homology of the sequenceof the antibody with a “standard” Kabat numbered sequence.

The phrase “substantially similar,” or “substantially the same”, as usedherein, denotes a sufficiently high degree of similarity between twonumeric values (generally one associated with an antibody of theinvention and the other associated with a reference/comparator antibody)such that one of skill in the art would consider the difference betweenthe two values to be of little or no biological and/or statisticalsignificance within the context of the biological characteristicmeasured by said values (e.g., Kd values). The difference between saidtwo values is preferably less than about 50%, preferably less than about40%, preferably less than about 30%, preferably less than about 20%,preferably less than about 10% as a function of the value for thereference/comparator antibody.

“Binding affinity” generally refers to the strength of the sum total ofnoncovalent interactions between a single binding site of a molecule(e.g., an antibody) and its binding partner (e.g., an antigen). Unlessindicated otherwise, as used herein, “binding affinity” refers tointrinsic binding affinity which reflects a 1:1 interaction betweenmembers of a binding pair (e.g., antibody and antigen). The affinity ofa molecule X for its partner Y can generally be represented by thedissociation constant (Kd). Affinity can be measured by common methodsknown in the art, including those described herein. Low-affinityantibodies generally bind antigen slowly and tend to dissociate readily,whereas high-affinity antibodies generally bind antigen faster and tendto remain bound longer. A variety of methods of measuring bindingaffinity are known in the art, any of which can be used for purposes ofthe present invention. Specific illustrative embodiments are describedin the following.

In one embodiment, the “Kd” or “Kd value” according to this invention ismeasured by a radiolabeled antigen binding assay (RIA) performed withthe Fab version of an antibody of interest and its antigen as describedby the following assay that measures solution binding affinity of Fabsfor antigen by equilibrating Fab with a minimal concentration of(¹²⁵I)-labeled antigen in the presence of a titration series ofunlabeled antigen, then capturing bound antigen with an anti-Fabantibody-coated plate (Chen, et al., (1999) J. Mol. Biol 293:865-881).To establish conditions for the assay, microtiter plates (Dynex) arecoated overnight with 5 ug/ml of a capturing anti-Fab antibody (CappelLabs) in 50 mM sodium carbonate (pH 9.6), and subsequently blocked with2% (w/v) bovine serum albumin in PBS for two to five hours at roomtemperature (approximately 23° C.). In a non-adsorbent plate (Nunc#269620), 100 pM or 26 pM [¹²⁵I]-antigen are mixed with serial dilutionsof a Fab of interest (e.g., consistent with assessment of an anti-VEGFantibody, Fab-12, in Presta et al., (1997) Cancer Res. 57:4593-4599).The Fab of interest is then incubated overnight; however, the incubationmay continue for a longer period (e.g., 65 hours) to insure thatequilibrium is reached. Thereafter, the mixtures are transferred to thecapture plate for incubation at room temperature (e.g., for one hour).The solution is then removed and the plate washed eight times with 0.1%Tween-20 in PBS. When the plates have dried, 150 ul/well of scintillant(MicroScint-20; Packard) is added, and the plates are counted on aTopcount gamma counter (Packard) for ten minutes. Concentrations of eachFab that give less than or equal to 20% of maximal binding are chosenfor use in competitive binding assays. According to another embodimentthe Kd or Kd value is measured by using surface plasmon resonance assaysusing a BIAcore™-2000 or a BIAcore™-3000 (BIAcore, Inc., Piscataway,N.J.) at 25 C with immobilized antigen CM5 chips at ˜10 response units(RU). Briefly, carboxymethylated dextran biosensor chips (CM5, BIAcoreInc.) are activated with N-ethyl-N′-(3-dimethylaminopropyl)-carbodiimidehydrochloride (EDC) and N-hydroxysuccinimide (NHS) according to thesupplier's instructions. Antigen is diluted with 10 mM sodium acetate,pH 4.8, into 5 ug/ml (˜0.2 uM) before injection at a flow rate of 5ul/minute to achieve approximately 10 response units (RU) of coupledprotein. Following the injection of antigen, 1M ethanolamine is injectedto block unreacted groups. For kinetics measurements, two-fold serialdilutions of Fab (0.78 nM to 500 nM) are injected in PBS with 0.05%Tween 20 (PBST) at 25° C. at a flow rate of approximately 25 ul/min.Association rates (k_(on)) and dissociation rates (k_(off)) arecalculated using a simple one-to-one Langmuir binding model (BIAcoreEvaluation Software version 3.2) by simultaneous fitting the associationand dissociation sensorgram. The equilibrium dissociation constant (Kd)is calculated as the ratio k_(off)/k_(on). See, e.g., Chen, Y., et al.,(1999) J. Mol. Biol 293:865-881. If the on-rate exceeds 10⁶ M⁻¹ S⁻¹ bythe surface plasmon resonance assay above, then the on-rate can bedetermined by using a fluorescent quenching technique that measures theincrease or decrease in fluorescence emission intensity (excitation=295nm; emission=340 nm, 16 nm band-pass) at 25° C. of a 20 nM anti-antigenantibody (Fab form) in PBS, pH 7.2, in the presence of increasingconcentrations of antigen as measured in a spectrometer, such as astop-flow equipped spectrophometer (Aviv Instruments) or a 8000-seriesSLM-Aminco spectrophotometer (ThermoSpectronic) with a stir red cuvette.

An “on-rate” or “rate of association” or “association rate” or “k_(on)”according to this invention can also be determined with the same surfaceplasmon resonance technique described above using a BIAcore™-2000 or aBIAcore™-3000 (BIAcore, Inc., Piscataway, N.J.) at 25 C with immobilizedantigen CM5 chips at 10 response units (RU). Briefly, carboxymethylateddextran biosensor chips (CM5, BIAcore Inc.) are activated withN-ethyl-N′-(3-dimethylaminopropyl)-carbodiimide hydrochloride (EDC) andN-hydroxysuccinimide (NHS) according to the supplier's instructions.Antigen is diluted with 10 mM sodium acetate, pH 4.8, into 5 ug/ml (˜0.2uM) before injection at a flow rate of 5 ul/minute to achieveapproximately 10 response units (RU) of coupled protein. Following theinjection of antigen, 1M ethanolamine is injected to block unreactedgroups. For kinetics measurements, two-fold serial dilutions of Fab(0.78 nM to 500 nM) are injected in PBS with 0.05% Tween 20 (PBST) at25° C. at a flow rate of approximately 25 ul/min. Association rates(k_(on)) and dissociation rates (k_(off)) are calculated using a simpleone-to-one Langmuir binding model (BIAcore Evaluation Software version3.2) by simultaneous fitting the association and dissociationsensorgram. The equilibrium dissociation constant (Kd) was calculated asthe ratio k_(off)/k_(on). See, e.g., Chen, Y., et al., (1999) J. Mol.Biol 293:865-881. However, if the on-rate exceeds 10⁶ M⁻¹ s⁻¹ by thesurface plasmon resonance assay above, then the on-rate is preferablydetermined by using a fluorescent quenching technique that measures theincrease or decrease in fluorescence emission intensity (excitation=295nm; emission=340 nm, 16 nm band-pass) at 25° C. of a 20 nM anti-antigenantibody (Fab form) in PBS, pH 7.2, in the presence of increasingconcentrations of antigen as measured in a spectrometer, such as astop-flow equipped spectrophometer (Aviv Instruments) or a 8000-seriesSLM-Aminco spectrophotometer (ThermoSpectronic) with a stirred cuvette.

The term “vector,” as used herein, is intended to refer to a nucleicacid molecule capable of transporting another nucleic acid to which ithas been linked. One type of vector is a “plasmid”, which refers to acircular double stranded DNA loop into which additional DNA segments maybe ligated. Another type of vector is a phage vector. Another type ofvector is a viral vector, wherein additional DNA segments may be ligatedinto the viral genome. Certain vectors are capable of autonomousreplication in a host cell into which they are introduced (e.g.,bacterial vectors having a bacterial origin of replication and episomalmammalian vectors). Other vectors (e.g., non-episomal mammalian vectors)can be integrated into the genome of a host cell upon introduction intothe host cell, and thereby are replicated along with the host genome.Moreover, certain vectors are capable of directing the expression ofgenes to which they are operatively linked. Such vectors are referred toherein as “recombinant expression vectors” (or simply, “recombinantvectors”). In general, expression vectors of utility in recombinant DNAtechniques are often in the form of plasmids. In the presentspecification, “plasmid” and “vector” may be used interchangeably as theplasmid is the most commonly used form of vector.

“Polynucleotide,” or “nucleic acid,” as used interchangeably herein,refer to polymers of nucleotides of any length, and include DNA and RNA.The nucleotides can be deoxyribonucleotides, ribonucleotides, modifiednucleotides or bases, and/or their analogs, or any substrate that can beincorporated into a polymer by DNA or RNA polymerase, or by a syntheticreaction. A polynucleotide may comprise modified nucleotides, such asmethylated nucleotides and their analogs. If present, modification tothe nucleotide structure may be imparted before or after assembly of thepolymer. The sequence of nucleotides may be interrupted bynon-nucleotide components. A polynucleotide may be further modifiedafter synthesis, such as by conjugation with a label. Other types ofmodifications include, for example, “caps”, substitution of one or moreof the naturally occurring nucleotides with an analog, internucleotidemodifications such as, for example, those with uncharged linkages (e.g.,methyl phosphonates, phosphotriesters, phosphoamidates, carbamates,etc.) and with charged linkages (e.g., phosphorothioates,phosphorodithioates, etc.), those containing pendant moieties, such as,for example, proteins (e.g., nucleases, toxins, antibodies, signalpeptides, ply-L-lysine, etc.), those with intercalators (e.g., acridine,psoralen, etc.), those containing chelators (e.g., metals, radioactivemetals, boron, oxidative metals, etc.), those containing alkylators,those with modified linkages (e.g., alpha anomeric nucleic acids, etc.),as well as unmodified forms of the polynucleotide(s). Further, any ofthe hydroxyl groups ordinarily present in the sugars may be replaced,for example, by phosphonate groups, phosphate groups, protected bystandard protecting groups, or activated to prepare additional linkagesto additional nucleotides, or may be conjugated to solid or semi-solidsupports. The 5′ and 3′ terminal OH can be phosphorylated or substitutedwith amines or organic capping group moieties of from 1 to 20 carbonatoms. Other hydroxyls may also be derivatized to standard protectinggroups. Polynucleotides can also contain analogous forms of ribose ordeoxyribose sugars that are generally known in the art, including, forexample, 2′-O-methyl-, 2′-O-allyl, 2′-fluoro- or 2′-azido-ribose,carbocyclic sugar analogs, alpha-anomeric sugars, epimeric sugars suchas arabinose, xyloses or lyxoses, pyranose sugars, furanose sugars,sedoheptuloses, acyclic analogs and a basic nucleoside analogs such asmethyl riboside. One or more phosphodiester linkages may be replaced byalternative linking groups. These alternative linking groups include,but are not limited to, embodiments wherein phosphate is replaced byP(O)S(“thioate”), P(S)S (“dithioate”), “(O)NR₂ (“amidate”), P(O)R,P(O)OR′, CO or CH₂ (“formacetal”), in which each R or R′ isindependently H or substituted or unsubstituted alkyl (1-20 C)optionally containing an ether (—O—) linkage, aryl, alkenyl, cycloalkyl,cycloalkenyl or araldyl. Not all linkages in a polynucleotide need beidentical. The preceding description applies to all polynucleotidesreferred to herein, including RNA and DNA.

“Oligonucleotide,” as used herein, generally refers to short, generallysingle stranded, generally synthetic polynucleotides that are generally,but not necessarily, less than about 200 nucleotides in length. Theterms “oligonucleotide” and “polynucleotide” are not mutually exclusive.The description above for polynucleotides is equally and fullyapplicable to oligonucleotides.

The term “EphB2” (interchangeably termed “EphB2R”), as used herein,refers, unless specifically or contextually indicated otherwise, to anynative or variant (whether native or synthetic) EphB2 polypeptide. Theterm “native sequence” specifically encompasses naturally occurringtruncated or secreted forms (e.g., an extracellular domain sequence),naturally occurring variant forms (e.g., alternatively spliced forms)and naturally-occurring allelic variants. The term “wild type EphB2”generally refers to a polypeptide comprising the amino acid sequence ofa naturally occurring EphB2 protein. The term “wild type EphB2 sequence”generally refers to an amino acid sequence found in a naturallyoccurring EphB2.

The terms “antibody” and “immunoglobulin” are used interchangeably inthe broadest sense and include monoclonal antibodies (for e.g., fulllength or intact monoclonal antibodies), polyclonal antibodies,multivalent antibodies, multispecific antibodies (e.g., bispecificantibodies so long as they exhibit the desired biological activity) andmay also include certain antibody fragments (as described in greaterdetail herein). An antibody can be human, humanized and/or affinitymatured.

The term “variable” refers to the fact that certain portions of thevariable domains differ extensively in sequence among antibodies and areused in the binding and specificity of each particular antibody for itsparticular antigen. However, the variability is not evenly distributedthroughout the variable domains of antibodies. It is concentrated inthree segments called complementarity-determining regions (CDRs) orhypervariable regions both in the light-chain and the heavy-chainvariable domains. The more highly conserved portions of variable domainsare called the framework (FR). The variable domains of native heavy andlight chains each comprise four FR regions, largely adopting a α-sheetconfiguration, connected by three CDRs, which form loops connecting, andin some cases forming part of, the α-sheet structure. The CDRs in eachchain are held together in close proximity by the FR regions and, withthe CDRs from the other chain, contribute to the formation of theantigen-binding site of antibodies (see Kabat et al, Sequences ofProteins of Immunological Interest, Fifth Edition, National Institute ofHealth, Bethesda, Md. (1991)). The constant domains are not involveddirectly in binding an antibody to an antigen, but exhibit variouseffector functions, such as participation of the antibody inantibody-dependent cellular toxicity.

Papain digestion of antibodies produces two identical antigen-bindingfragments, called “Fab” fragments, each with a single antigen-bindingsite, and a residual “Fc” fragment, whose name reflects its ability tocrystallize readily. Pepsin treatment yields an F(ab′)₂ fragment thathas two antigen-combining sites and is still capable of cross-linkingantigen.

“Fv” is the minimum antibody fragment which contains a completeantigen-recognition and -binding site. In a two-chain Fv species, thisregion consists of a dimer of one heavy- and one light-chain variabledomain in tight, non-covalent association. In a single-chain Fv species,one heavy- and one light-chain variable domain can be covalently linkedby a flexible peptide linker such that the light and heavy chains canassociate in a “dimeric” structure analogous to that in a two-chain Fvspecies. It is in this configuration that the three CDRs of eachvariable domain interact to define an antigen-binding site on thesurface of the VH-VL dimer. Collectively, the six CDRs conferantigen-binding specificity to the antibody. However, even a singlevariable domain (or half of an Fv comprising only three CDRs specificfor an antigen) has the ability to recognize and bind antigen, althoughat a lower affinity than the entire binding site.

The Fab fragment also contains the constant domain of the light chainand the first constant domain (CH1) of the heavy chain. Fab′ fragmentsdiffer from Fab fragments by the addition of a few residues at thecarboxy terminus of the heavy chain CH1 domain including one or morecysteines from the antibody hinge region. Fab′-SH is the designationherein for Fab′ in which the cysteine residue(s) of the constant domainsbear a free thiol group. F(ab′)₂ antibody fragments originally wereproduced as pairs of Fab′ fragments which have hinge cysteines betweenthem. Other chemical couplings of antibody fragments are also known.

The “light chains” of antibodies (immunoglobulins) from any vertebratespecies can be assigned to one of two clearly distinct types, calledkappa (κ) and lambda (λ), based on the amino acid sequences of theirconstant domains.

Depending on the amino acid sequence of the constant domain of theirheavy chains, immunoglobulins can be assigned to different classes.There are five major classes of immunoglobulins: IgA, IgD, IgE, IgG, andIgM, and several of these can be further divided into subclasses(isotypes), e.g., IgG₁, IgG₂, IgG₃, IgG₄, IgA₁, and IgA₂. Theheavy-chain constant domains that correspond to the different classes ofimmunoglobulins are called α, δ, ε, γ, and μ, respectively. The subunitstructures and three-dimensional configurations of different classes ofimmunoglobulins are well known.

“Antibody fragments” comprise only a portion of an intact antibody,wherein the portion preferably retains at least one, preferably most orall, of the functions normally associated with that portion when presentin an intact antibody. In one embodiment, an antibody fragment comprisesan antigen binding site of the intact antibody and thus retains theability to bind antigen. In another embodiment, an antibody fragment,for example one that comprises the Fc region, retains at least one ofthe biological functions normally associated with the Fc region whenpresent in an intact antibody, such as FcRn binding, antibody half lifemodulation, ADCC function and complement binding. In one embodiment, anantibody fragment is a monovalent antibody that has an in vivo half lifesubstantially similar to an intact antibody. For e.g., such an antibodyfragment may comprise on antigen binding arm linked to an Fc sequencecapable of conferring in vivo stability to the fragment.

The term “monoclonal antibody” as used herein refers to an antibody froma population of substantially homogeneous antibodies, i.e., theindividual antibodies comprising the population are identical and/orbind the same epitope(s), except for possible variants that may ariseduring production of the monoclonal antibody, such variants generallybeing present in minor amounts. Such monoclonal antibody typicallyincludes an antibody comprising a polypeptide sequence that binds atarget, wherein the target-binding polypeptide sequence was obtained bya process that includes the selection of a single target bindingpolypeptide sequence from a plurality of polypeptide sequences. Forexample, the selection process can be the selection of a unique clonefrom a plurality of clones, such as a pool of hybridoma clones, phageclones or recombinant DNA clones. It should be understood that theselected target binding sequence can be further altered, for example, toimprove affinity for the target, to humanize the target bindingsequence, to improve its production in cell culture, to reduce itsimmunogenicity in vivo, to create a multispecific antibody, etc., andthat an antibody comprising the altered target binding sequence is alsoa monoclonal antibody of this invention. In contrast to polyclonalantibody preparations which typically include different antibodiesdirected against different determinants (epitopes), each monoclonalantibody of a monoclonal antibody preparation is directed against asingle determinant on an antigen. In addition to their specificity, themonoclonal antibody preparations are advantageous in that they aretypically uncontaminated by other immunoglobulins. The modifier“monoclonal” indicates the character of the antibody as being obtainedfrom a substantially homogeneous population of antibodies, and is not tobe construed as requiring production of the antibody by any particularmethod. For example, the monoclonal antibodies to be used in accordancewith the present invention may be made by a variety of techniques,including, for example, the hybridoma method (e.g., Kohler et al,Nature, 256:495 (1975); Harlow et al, Antibodies: A Laboratory Manual,(Cold Spring Harbor Laboratory Press, 2nd ed. 1988); Hammerling et al.,in: Monoclonal Antibodies and T-Cell Hybridomas 563-681, (Elsevier,N.Y., 1981)), recombinant DNA methods (see, e.g., U.S. Pat. No.4,816,567), phage display technologies (see, e.g., Clackson et al.,Nature, 352:624-628 (1991); Marks et al, J. Mol. Biol., 222:581-597(1991); Sidhu et al., J. Mol. Biol. 338(2):299-310 (2004); Lee et al.,J. Mol. Biol. 340(5): 1073-1093 (2004); Fellouse, Proc. Nat. Acad. Sci.USA 101(34):12467-12472 (2004); and Lee et al. J. Immunol. Methods284(1-2): 119-132 (2004), and technologies for producing human orhuman-like antibodies in animals that have parts or all of the humanimmunoglobulin loci or genes encoding human immunoglobulin sequences(see, e.g., WO 1998/24893; WO 1996/34096; WO 1996/33735; WO 1991/10741;Jakobovits et al., Proc. Natl. Acad. Sci. USA, 90:2551 (1993);Jakobovits et al., Nature, 362:255-258 (1993); Bruggemann et al., Yearin Immuno., 7:33 (1993); U.S. Pat. Nos. 5,545,806; 5,569,825; 5,591,669(all of GenPharm); 5,545,807; WO 1997/17852; U.S. Pat. Nos. 5,545,807;5,545,806; 5,569,825; 5,625,126; 5,633,425; and 5,661,016; Marks et al.,Bio/Technology, 10: 779-783 (1992); Lonberg et al., Nature, 368: 856-859(1994); Morrison, Nature, 368: 812-813 (1994); Fishwild et al., NatureBiotechnology, 14: 845-851 (1996); Neuberger, Nature Biotechnology, 14:826 (1996); and Lonberg and Huszar, Intern. Rev. Immunol., 13: 65-93(1995).

“Humanized” forms of non-human (e.g., murine) antibodies are chimericantibodies that contain minimal sequence derived from non-humanimmunoglobulin. For the most part, humanized antibodies are humanimmunoglobulins (recipient antibody) in which residues from ahypervariable region of the recipient are replaced by residues from ahypervariable region of a non-human species (donor antibody) such asmouse, rat, rabbit or nonhuman primate having the desired specificity,affinity, and capacity. In some instances, framework region (FR)residues of the human immunoglobulin are replaced by correspondingnon-human residues. Furthermore, humanized antibodies may compriseresidues that are not found in the recipient antibody or in the donorantibody. These modifications are made to further refine antibodyperformance. In general, the humanized antibody will comprisesubstantially all of at least one, and typically two, variable domains,in which all or substantially all of the hypervariable loops correspondto those of a non-human immunoglobulin and all or substantially all ofthe FRs are those of a human immunoglobulin sequence. The humanizedantibody optionally will also comprise at least a portion of animmunoglobulin constant region (Fc), typically that of a humanimmunoglobulin. For further details, see Jones et al., Nature321:522-525 (1986); Riechmann et al., Nature 332:323-329 (1988); andPresta, Curr. Op. Struct. Biol. 2:593-596 (1992). See also the followingreview articles and references cited therein: Vaswani and Hamilton, Ann.Allergy, Asthma & Immunol. 1:105-115 (1998); Harris, Biochem. Soc.Transactions 23:1035-1038 (1995); Hurle and Gross, Curr. Op. Biotech.5:428-433 (1994).

“Chimeric” antibodies (immunoglobulins) have a portion of the heavyand/or light chain identical with or homologous to correspondingsequences in antibodies derived from a particular species or belongingto a particular antibody class or subclass, while the remainder of thechain(s) is identical with or homologous to corresponding sequences inantibodies derived from another species or belonging to another antibodyclass or subclass, as well as fragments of such antibodies, so long asthey exhibit the desired biological activity (U.S. Pat. No. 4,816,567;and Morrison et al., Proc. Natl. Acad. Sci. USA 81:6851-6855 (1984)).Humanized antibody as used herein is a subset of chimeric antibodies.

An “antigen” is a predetermined antigen to which an antibody canselectively bind. The target antigen may be polypeptide, carbohydrate,nucleic acid, lipid, hapten or other naturally occurring or syntheticcompound. Preferably, the target antigen is a polypeptide.

The term “hypervariable region”, “HVR”, or “HV”, when used herein refersto the regions of an antibody variable domain which are hypervariable insequence and/or form structurally defined loops. Generally, antibodiescomprise six hypervariable regions; three in the VH(H1, H2, H3), andthree in the VL (L1, L2, L3). A number of hypervariable regiondelineations are in use and are encompassed herein. The KabatComplementarity Determining Regions (CDRs) are based on sequencevariability and are the most commonly used (Kabat et al., Sequences ofProteins of Immunological Interest, 5th Ed. Public Health Service,National Institutes of Health, Bethesda, Md. (1991)). Chothia refersinstead to the location of the structural loops (Chothia and Lesk J.Mol. Biol. 196:901-917 (1987)). The AbM hypervariable regions representa compromise between the Kabat CDRs and Chothia structural loops, andare used by Oxford Molecular's AbM antibody modeling software. The“contact” hypervariable regions are based on an analysis of theavailable complex crystal structures. The residues from the Kabat,Chothia and contact hypervariable regions are noted below.

Loop Kabat Chothia Contact L1 L24-L34 L24-L34 L30-L36 L2 L50-L56 L50-L56L46-L55 L3 L89-L97 L89-L97 L89-L96 H1 H31-H35B H26-H32 H30-H35B (KabatNumbering) H2 H50-H65 H52-H56 H47-H58 H3 H95-H102 H95-H102 H93-H101

Hypervariable regions may comprise “extended hypervariable regions” asfollows: 24-36 or 24-34 (L1), 46-56 or 50-56 (L2) and 89-97 or 89-96(L3) in the VL and 26-35 (H1), 50-65 or 49-65 (H2) and 93-102, 94-102 or95-102 (H3) in the VH. The variable domain residues are numberedaccording to Kabat et al., supra for each of these definitions.

“Framework” or “FR” residues are those variable domain residues otherthan the hypervariable region residues as herein defined.

“Single-chain Fv” or “scFv” antibody fragments comprise the VH and VLdomains of antibody,

wherein these domains are present in a single polypeptide chain.Generally, the scFv polypeptide further comprises a polypeptide linkerbetween the VH and VL domains which enables the scFv to form the desiredstructure for antigen binding. For a review of scFv see Pluckthun, inThe Pharmacology of Monoclonal Antibodies, vol. 113, Rosenburg and Mooreeds., Springer-Verlag, New York, pp. 269-315 (1994).

The term “diabodies” refers to small antibody fragments with twoantigen-binding sites, which fragments comprise a heavy-chain variabledomain (VH) connected to a light-chain variable domain (VL) in the samepolypeptide chain (VH−VL). By using a linker that is too short to allowpairing between the two domains on the same chain, the domains areforced to pair with the complementary domains of another chain andcreate two antigen-binding sites. Diabodies are described more fully in,for example, EP 404,097; WO 93/11161; and Hollinger et al, Proc. Natl.Acad. Sci. USA, 90:6444-6448 (1993).

A “human antibody” is one which possesses an amino acid sequence whichcorresponds to that of an antibody produced by a human and/or has beenmade using any of the techniques for making human antibodies asdisclosed herein. This definition of a human antibody specificallyexcludes a humanized antibody comprising non-human antigen-bindingresidues.

An “affinity matured” antibody is one with one or more alterations inone or more CDRs thereof which result in an improvement in the affinityof the antibody for antigen, compared to a parent antibody which doesnot possess those alteration(s). Preferred affinity matured antibodieswill have nanomolar or even picomolar affinities for the target antigen.Affinity matured antibodies are produced by procedures known in the art.Marks et al. Bio/Technology 10:779-783 (1992) describes affinitymaturation by VH and VL domain shuffling. Random mutagenesis of CDRand/or framework residues is described by: Barbas et al. Proc Nat. Acad.Sci, USA 91:3809-3813 (1994); Schier et al. Gene 169:147-155 (1995);Yelton et al. J. Immunol. 155:1994-2004 (1995); Jackson et al., J.Immunol. 154(7):3310-9 (1995); and Hawkins et al, J. Mol. Biol.226:889-896 (1992).

Antibody “effector functions” refer to those biological activitiesattributable to the Fc region (a native sequence Fc region or amino acidsequence variant Fc region) of an antibody, and vary with the antibodyisotype. Examples of antibody effector functions include: C1q bindingand complement dependent cytotoxicity; Fc receptor binding;antibody-dependent cell-mediated cytotoxicity (ADCC); phagocytosis; downregulation of cell surface receptors (e.g. B cell receptor); and B cellactivation.

Antibody-dependent cell-mediated cytotoxicity” or “ADCC” refers to aform of cytotoxicity in which secreted Ig bound onto Fc receptors (FcRs)present on certain cytotoxic cells (e.g. Natural Killer (NK) cells,neutrophils, and macrophages) enable these cytotoxic effector cells tobind specifically to an antigen-bearing target cell and subsequentlykill the target cell with cytotoxins. The antibodies “arm” the cytotoxiccells and are absolutely required for such killing. The primary cellsfor mediating ADCC, NK cells, express FcγRIII only, whereas monocytesexpress FcγRI, FcγRII and FcγRIII. FcR expression on hematopoietic cellsis summarized in Table 3 on page 464 of Ravetch and Kinet, Annu. Rev.Immunol 9:457-92 (1991). To assess ADCC activity of a molecule ofinterest, an in vitro ADCC assay, such as that described in U.S. Pat.No. 5,500,362 or 5,821,337 or Presta U.S. Pat. No. 6,737,056 may beperformed. Useful effector cells for such assays include peripheralblood mononuclear cells (PBMC) and Natural Killer (NK) cells.Alternatively, or additionally, ADCC activity of the molecule ofinterest may be assessed in vivo, e.g., in a animal model such as thatdisclosed in Clynes et al. PNAS (USA) 95:652-656 (1998).

“Human effector cells” are leukocytes which express one or more FcRs andperform effector functions. Preferably, the cells express at leastFcγRIII and perform ADCC effector function. Examples of human leukocyteswhich mediate ADCC include peripheral blood mononuclear cells (PBMC),natural killer (NK) cells, monocytes, cytotoxic T cells and neutrophils;with PBMCs and NK cells being preferred. The effector cells may beisolated from a native source, e.g. from blood.

“Fc receptor” or “FcR” describes a receptor that binds to the Fc regionof an antibody. The preferred FcR is a native sequence human FcR.Moreover, a preferred FcR is one which binds an IgG antibody (a gammareceptor) and includes receptors of the FcγRI, FcγRII, and FcγRIIIsubclasses, including allelic variants and alternatively spliced formsof these receptors. FcγRII receptors include FcγRIIA (an “activatingreceptor”) and FcγRIIB (an “inhibiting receptor”), which have similaramino acid sequences that differ primarily in the cytoplasmic domainsthereof. Activating receptor FcγRIIA contains an immunoreceptortyrosine-based activation motif (ITAM) in its cytoplasmic domain.Inhibiting receptor FcγRIIB contains an immunoreceptor tyrosine-basedinhibition motif (ITIM) in its cytoplasmic domain. (see review M. inDaëron Annu. Rev. Immunol. 15:203-234 (1997)). FcRs are reviewed inRavetch and Kinet, Annu. Rev. Immunol 9:457-92 (1991); Capel et al.,Immunomethods 4:25-34 (1994); and de Haas et al., J. Lab. Clin. Med.126:330-41 (1995). Other FcRs, including those to be identified in thefuture, are encompassed by the term “FcR” herein. The term also includesthe neonatal receptor, FcRn, which is responsible for the transfer ofmaternal IgGs to the fetus (Guyer et al, J. Immunol. 117:587 (1976) andKim et al., J. Immunol. 24:249 (1994)) and regulates homeostasis ofimmunoglobulins.

WO00/42072 (Presta) describes antibody variants with improved ordiminished binding to FcRs. The content of that patent publication isspecifically incorporated herein by reference. See, also, Shields et alJ. Biol. Chem. 9(2): 6591-6604 (2001).

Methods of measuring binding to FcRn are known (see, e.g., Ghetie 1997,Hinton 2004). Binding to human FcRn in vivo and serum half life of humanFcRn high affinity binding polypeptides can be assayed, e.g., intransgenic mice or transfected human cell lines expressing human FcRn,or in primates administered with the Fc variant polypeptides.

“Complement dependent cytotoxicity” or “CDC” refers to the lysis of atarget cell in the presence of complement. Activation of the classicalcomplement pathway is initiated by the binding of the first component ofthe complement system (C1q) to antibodies (of the appropriate subclass)which are bound to their cognate antigen. To assess complementactivation, a CDC assay, e.g. as described in Gazzano-Santoro et al., J.Immunol. Methods 202:163 (1996), may be performed.

Polypeptide variants with altered Fc region amino acid sequences andincreased or decreased C1q binding capability are described in U.S. Pat.No. 6,194,551B1 and WO99/51642. The contents of those patentpublications are specifically incorporated herein by reference. See,also, Idusogie et al J. Immunol. 164: 4178-4184 (2000).

A “disorder” or “disease” is any condition that would benefit fromtreatment with a substance/molecule or method of the invention. Thisincludes chronic and acute disorders or diseases including thosepathological conditions which predispose the mammal to the disorder inquestion. Non-limiting examples of disorders to be treated hereininclude malignant and benign tumors; carcinoma, blastoma, and sarcoma.

The terms “cell proliferative disorder” and “proliferative disorder”refer to disorders that are associated with some degree of abnormal cellproliferation. In one embodiment, the cell proliferative disorder iscancer.

“Tumor”, as used herein, refers to all neoplastic cell growth andproliferation, whether malignant or benign, and all pre-cancerous andcancerous cells and tissues. The terms “cancer”, “cancerous”, “cellproliferative disorder”, “proliferative disorder” and “tumor” are notmutually exclusive as referred to herein.

The terms “cancer” and “cancerous” refer to or describe thephysiological condition in mammals that is typically characterized byunregulated cell growth/proliferation. Examples of cancer include butare not limited to, carcinoma, lymphoma, blastoma, sarcoma, andleukemia. More particular examples of such cancers include squamous cellcancer, small-cell lung cancer, non-small cell lung cancer,adenocarcinoma of the lung, squamous carcinoma of the lung, cancer ofthe peritoneum, hepatocellular cancer, gastrointestinal cancer,pancreatic cancer, glioblastoma, cervical cancer, ovarian cancer, livercancer, bladder cancer, hepatoma, breast cancer, colon cancer,colorectal cancer, endometrial or uterine carcinoma, salivary glandcarcinoma, kidney cancer, liver cancer, prostate cancer, vulval cancer,thyroid cancer, hepatic carcinoma, gastric cancer, melanoma, and varioustypes of head and neck cancer. Dysregulation of angiogenesis can lead tomany disorders that can be treated by compositions and methods of theinvention. These disorders include both non-neoplastic and neoplasticconditions. Neoplastics include but are not limited those describedabove. Non-neoplastic disorders include but are not limited to undesiredor aberrant hypertrophy, arthritis, rheumatoid arthritis (RA),psoriasis, psoriatic plaques, sarcoidosis, atherosclerosis,atherosclerotic plaques, diabetic and other proliferative retinopathiesincluding retinopathy of prematurity, retrolental fibroplasia,neovascular glaucoma, age-related macular degeneration, diabetic macularedema, corneal neovascularization, corneal graft neovascularization,corneal graft rejection, retinauchoroidal neovascularization,neovascularization of the angle (rubeosis), ocular neovascular disease,vascular restenosis, arteriovenous malformations (AVM), meningioma,hemangioma, angiofibroma, thyroid hyperplasias (including Grave'sdisease), corneal and other tissue transplantation, chronicinflammation, lung inflammation, acute lung injury/ARDS, sepsis, primarypulmonary hypertension, malignant pulmonary effusions, cerebral edema(e.g., associated with acute stroke/closed head injury/trauma), synovialinflammation, pannus formation in RA, myositis ossificans, hypertropicbone formation, osteoarthritis (OA), refractory ascites, polycysticovarian disease, endometriosis, 3rd spacing of fluid diseases(pancreatitis, compartment syndrome, burns, bowel disease), uterinefibroids, premature labor, chronic inflammation such as IBD (Crohn'sdisease and ulcerative colitis), renal allograft rejection, inflammatorybowel disease, nephrotic syndrome, undesired or aberrant tissue massgrowth (non-cancer), hemophilic joints, hypertrophic scars, inhibitionof hair growth, Osler-Weber syndrome, pyogenic granuloma retrolentalfibroplasias, scleroderma, trachoma, vascular adhesions, synovitis,dermatitis, preeclampsia, ascites, pericardial effusion (such as thatassociated with pericarditis), and pleural effusion.

The terms “neurodegenerative disease” and “neurodegenerative disorder”are used in the broadest sense to include all disorders the pathology ofwhich involves neuronal degeneration and/or dysfunction, including,without limitation, peripheral neuropathies; motomeuron disorders, suchas amylotrophic lateral sclerosis (ALS, Lou Gehrig's disease), Bell'spalsy, and various conditions involving spinal muscular atrophy orparalysis; and other human neurodegenerative diseases, such asAlzheimer's disease, Parkinson's disease, epilepsy, multiple sclerosis,Huntington's chorea, Down's Syndrome, nerve deafness, and Meniere'sdisease.

“Peripheral neuropathy” is a neurodegenerative disorder that affects theperipheral nerves, most often manifested as one or a combination ofmotor, sensory, sensorimotor, or autonomic dysfunction. Peripheralneuropathies may, for example, be genetically acquired, can result froma systemic disease, or can be induced by a toxic agent, such as aneurotoxic drug, e.g. antineoplastic agent, or industrial orenvironmental pollutant. “Peripheral sensory neuropathy” ischaracterized by the degeneration of peripheral sensory neurons, whichmay be idiopathic, may occur, for example, as a consequence of diabetes(diabetic neuropathy), cytostatic drug therapy in cancer (e.g. treatmentwith chemotherapeutic agents such as vincristine, cisplatin,methotrexate, 3′-azido-3′-deoxythymidine, or taxanes, e.g. paclitaxel[TAXOL®, Bristol-Myers Squibb Oncology, Princeton, N.J.] and doxetaxel[TAXOTER®, Rhône-Poulenc Rorer, Antony, France]), alcoholism, acquiredimmunodeficiency syndrom (AIDS), or genetic predisposition. Geneticallyacquired peripheral neuropathies include, for example, Refsum's disease,Krabbe's disease, Metachromatic leukodystrophy, Fabry's disease,Dejerine-Sottas syndrome, Abetalipoproteinemia, and Charcot-Marie-Tooth(CMT) Disease (also known as Proneal Muscular Atrophy or HereditaryMotor Sensory Neuropathy (HMSN)). Most types of peripheral neuropathydevelop slowly, over the course of several months or years. In clinicalpractice such neuropathies are called chronic. Sometimes a peripheralneuropathy develops rapidly, over the course of a few days, and isreferred to as acute. Peripheral neuropathy usually affects sensory andmotor nerves together so as to cause a mixed sensory and motorneuropathy, but pure sensory and pure motor neuropathy are also known.

As used herein, “treatment” refers to clinical intervention in anattempt to alter the natural course of the individual or cell beingtreated, and can be performed either for prophylaxis or during thecourse of clinical pathology. Desirable effects of treatment includepreventing occurrence or recurrence of disease, alleviation of symptoms,diminishment of any direct or indirect pathological consequences of thedisease, preventing metastasis, decreasing the rate of diseaseprogression, amelioration or palliation of the disease state, andremission or improved prognosis. In some embodiments, antibodies of theinvention are used to delay development of a disease or disorder.

An “individual” is a vertebrate, preferably a mammal, more preferably ahuman. Mammals include, but are not limited to, farm animals (such ascows), sport animals, pets (such as cats, dogs and horses), primates,mice and rats.

“Mammal” for purposes of treatment refers to any animal classified as amammal, including humans, domestic and farm animals, and zoo, sports, orpet animals, such as dogs, horses, cats, cows, etc. Preferably, themammal is human.

An “effective amount” refers to an amount effective, at dosages and forperiods of time necessary, to achieve the desired therapeutic orprophylactic result.

A “therapeutically effective amount” of a substance/molecule of theinvention, agonist or antagonist may vary according to factors such asthe disease state, age, sex, and weight of the individual, and theability of the substance/molecule, agonist or antagonist to elicit adesired response in the individual. A therapeutically effective amountis also one in which any toxic or detrimental effects of thesubstance/molecule, agonist or antagonist are outweighed by thetherapeutically beneficial effects. A “prophylactically effectiveamount” refers to an amount effective, at dosages and for periods oftime necessary, to achieve the desired prophylactic result. Typicallybut not necessarily, since a prophylactic dose is used in subjects priorto or at an earlier stage of disease, the prophylactically effectiveamount will be less than the therapeutically effective amount.

The term “cytotoxic agent” as used herein refers to a substance thatinhibits or prevents the function of cells and/or causes destruction ofcells. The term is intended to include radioactive isotopes (e.g.,At²¹¹, I¹³¹, I¹²⁵, Y⁹⁰, Re¹⁸⁶, Re¹⁸⁸, Sm¹⁵³, Bi²¹², P³² and radioactiveisotopes of Lu), chemotherapeutic agents e.g. methotrexate, adriamicin,vinca alkaloids (vincristine, vinblastine, etoposide), doxorubicin,melphalan, mitomycin C, chlorambucil, daunorubicin or otherintercalating agents, enzymes and fragments thereof such as nucleolyticenzymes, antibiotics, and toxins such as small molecule toxins orenzymatically active toxins of bacterial, fungal, plant or animalorigin, including fragments and/or variants thereof, and the variousantitumor or anticancer agents disclosed below. Other cytotoxic agentsare described below. A tumoricidal agent causes destruction of tumorcells.

A “chemotherapeutic agent” is a chemical compound useful in thetreatment of cancer. Examples of chemotherapeutic agents includealkylating agents such as thiotepa and CYTOXAN® cyclosphosphamide; alkylsulfonates such as busulfan, improsulfan and piposulfan; aziridines suchas benzodopa, carboquone, meturedopa, and uredopa; ethylenimines andmethylamelamines including altretamine, triethylenemelamine,trietylenephosphoramide, triethiylenethiophosphoramide andtrimethylolomelamine; acetogenins (especially bullatacin andbullatacinone); delta-9-tetrahydrocannabinol (dronabinol, MARINOL®);beta-lapachone; lapachol; colchicines; betulinic acid; a camptothecin(including the synthetic analogue topotecan (HYCAMTIN®), CPT-11(irinotecan, CAMPTOSAR®), acetylcamptothecin, scopolectin, and9-aminocamptothecin); bryostatin; callystatin; CC-1065 (including itsadozelesin, carzelesin and bizelesin synthetic analogues);podophyllotoxin; podophyllinic acid; teniposide; cryptophycins(particularly cryptophycin 1 and cryptophycin 8); dolastatin;duocarmycin (including the synthetic analogues, KW-2189 and CB1-TM1);eleutherobin; pancratistatin; a sarcodictyin; spongistatin; nitrogenmustards such as chlorambucil, chlomaphazine, cholophosphamide,estramustine, ifosfamide, mechlorethamine, mechlorethamine oxidehydrochloride, melphalan, novembichin, phenesterine, prednimustine,trofosfamide, uracil mustard; nitrosureas such as carmustine,chlorozotocin, fotemustine, lomustine, nimustine, and ranimnustine;antibiotics such as the enediyne antibiotics (e.g., calicheamicin,especially calicheamicin gammalI and calicheamicin omegalI (see, e.g.,Agnew, Chem. Intl. Ed. Engl., 33: 183-186 (1994)); dynemicin, includingdynemicin A; an esperamicin; as well as neocarzinostatin chromophore andrelated chromoprotein enediyne antiobiotic chromophores),aclacinomysins, actinomycin, authramycin, azaserine, bleomycins,cactinomycin, carabicin, caminomycin, carzinophilin, chromomycinis,dactinomycin, daunorubicin, detorubicin, 6-diazo-5-oxo-L-norleucine,ADRIAMYCIN® doxorubicin (including morpholino-doxorubicin,cyanomorpholino-doxorubicin, 2-pyrrolino-doxorubicin anddeoxydoxorubicin), epirubicin, esorubicin, idarubicin, marcellomycin,mitomycins such as mitomycin C, mycophenolic acid, nogalamycin,olivomycins, peplomycin, potfiromycin, puromycin, quelamycin,rodorubicin, streptonigrin, streptozocin, tubercidin, ubenimex,zinostatin, zorubicin; anti-metabolites such as methotrexate and5-fluorouracil (5-FU); folic acid analogues such as denopterin,methotrexate, pteropterin, trimetrexate; purine analogs such asfludarabine, 6-mercaptopurine, thiamiprine, thioguanine; pyrimidineanalogs such as ancitabine, azacitidine, 6-azauridine, carmofur,cytarabine, dideoxyuridine, doxifluridine, enocitabine, floxuridine;androgens such as calusterone, dromostanolone propionate, epitiostanol,mepitiostane, testolactone; anti-adrenals such as aminoglutethimide,mitotane, trilostane; folic acid replenisher such as frolinic acid;aceglatone; aldophosphamide glycoside; aminolevulinic acid; eniluracil;amsacrine; bestrabucil; bisantrene; edatraxate; defofamine; demecolcine;diaziquone; elformithine; elliptinium acetate; an epothilone; etoglucid;gallium nitrate; hydroxyurea; lentinan; lonidainine; maytansinoids suchas maytansine and ansamitocins; mitoguazone; mitoxantrone; mopidanmol;nitraerine; pentostatin; phenamet; pirarubicin; losoxantrone;2-ethylhydrazide; procarbazine; PSK® polysaccharide complex (JHS NaturalProducts, Eugene, Oreg.); razoxane; rhizoxin; sizofuran; spirogermanium;tenuazonic acid; triaziquone; 2,2′,2″-trichlorotriethylamine;trichothecenes (especially T-2 toxin, verracurin A, roridin A andanguidine); urethan; vindesine (ELDISINE®, FILDESIN®); dacarbazine;mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine;arabinoside (“Ara-C”); thiotepa; taxoids, e.g., TAXOL® paclitaxel(Bristol-Myers Squibb Oncology, Princeton, N.J.), ABRAXANE™Cremophor-free, albumin-engineered nanoparticle formulation ofpaclitaxel (American Pharmaceutical Partners, Schaumberg, Ill.), andTAXOTERE® doxetaxel (Rhône-Poulenc Rorer, Antony, France); chloranbucil;gemcitabine (GEMZAR®); 6-thioguanine; mercaptopurine; methotrexate;platinum analogs such as cisplatin and carboplatin; vinblastine(VELBAN®); platinum; etoposide (VP-16); ifosfamide; mitoxantrone;vincristine (ONCOVIN®); oxaliplatin; leucovovin; vinorelbine(NAVELBINE®); novantrone; edatrexate; daunomycin; aminopterin;ibandronate; topoisomerase inhibitor RFS 2000; difluoromethylornithine(DMFO); retinoids such as retinoic acid; capecitabine (XELODA®);pharmaceutically acceptable salts, acids or derivatives of any of theabove; as well as combinations of two or more of the above such as CHOP,an abbreviation for a combined therapy of cyclophosphamide, doxorubicin,vincristine, and prednisolone, and FOLFOX, an abbreviation for atreatment regimen with oxaliplatin (ELOXATIN™) combined with 5-FU andleucovovin.

Also included in this definition are anti-hormonal agents that act toregulate, reduce, block, or inhibit the effects of hormones that canpromote the growth of cancer, and are often in the form of systemic, orwhole-body treatment. They may be hormones themselves. Examples includeanti-estrogens and selective estrogen receptor modulators (SERMs),including, for example, tamoxifen (including NOLVADEX® tamoxifen),EVISTA® raloxifene, droloxifene, 4-hydroxytamoxifen, trioxifene,keoxifene, LY117018, onapristone, and FARESTON® toremifene;anti-progesterones; estrogen receptor down-regulators (ERDs); agentsthat function to suppress or shut down the ovaries, for example,leutinizing hormone-releasing hormone (LHRH) agonists such as LUPRON®and ELIGARD® leuprolide acetate, goserelin acetate, buserelin acetateand tripterelin; other anti-androgens such as flutamide, nilutamide andbicalutamide; and aromatase inhibitors that inhibit the enzymearomatase, which regulates estrogen production in the adrenal glands,such as, for example, 4(5)-imidazoles, aminoglutethimide, MEGASE®megestrol acetate, AROMASIN® exemestane, formestanie, fadrozole,RIVISOR® vorozole, FEMARA® letrozole, and ARIMIDEX® anastrozole. Inaddition, such definition of chemotherapeutic agents includesbisphosphonates such as clodronate (for example, BONEFOS® or OSTAC®),DIDROCAL® etidronate, NE-58095, ZOMETA® zoledronic acid/zoledronate,FOSAMAX® alendronate, AREDIA® pamidronate, SKELID® tiludronate, orACTONEL® risedronate; as well as troxacitabine (a 1,3-dioxolanenucleoside cytosine analog); antisense oligonucleotides, particularlythose that inhibit expression of genes in signaling pathways implicatedin abherant cell proliferation, such as, for example, PKC-alpha, Raf,H-Ras, and epidermal growth factor receptor (EGF-R); vaccines such asTHERATOPE® vaccine and gene therapy vaccines, for example, ALLOVECTIN®vaccine, LEUVECTIN® vaccine, and VAXID® vaccine; LURTOTECAN®topoisomerase 1 inhibitor; ABARELIX® rmRH; lapatinib ditosylate (anErbB-2 and EGFR dual tyrosine kinase small-molecule inhibitor also knownas GW572016); and pharmaceutically acceptable salts, acids orderivatives of any of the above.

A “growth inhibitory agent” when used herein refers to a compound orcomposition which inhibits growth of a cell (such as a cell expressingEphB2) either in vitro or in vivo. Thus, the growth inhibitory agent maybe one which significantly reduces the percentage of cells (such as acell expressing EphB2) in S phase. Examples of growth inhibitory agentsinclude agents that block cell cycle progression (at a place other thanS phase), such as agents that induce G1 arrest and M-phase arrest.Classical M-phase blockers include the vincas (vincristine andvinblastine), taxanes, and topoisomerase II inhibitors such asdoxorubicin, epirubicin, daunorubicin, etoposide, and bleomycin. Thoseagents that arrest G1 also spill over into S-phase arrest, for example,DNA alkylating agents such as tamoxifen, prednisone, dacarbazine,mechlorethamine, cisplatin, methotrexate, 5-fluorouracil, and ara-C.Further information can be found in The Molecular Basis of Cancer,Mendelsohn and Israel, eds., Chapter 1, entitled “Cell cycle regulation,oncogenes, and antineoplastic drugs” by Murakami et al. (WB Saunders:Philadelphia, 1995), especially p. 13. The taxanes (paclitaxel anddocetaxel) are anticancer drugs both derived from the yew tree.Docetaxel (TAXOTERE®, Rhone-Poulenc Rorer), derived from the Europeanyew, is a semisynthetic analogue of paclitaxel (TAXOL®, Bristol-MyersSquibb). Paclitaxel and docetaxel promote the assembly of microtubulesfrom tubulin dimers and stabilize microtubules by preventingdepolymerization, which results in the inhibition of mitosis in cells.

“Doxorubicin” is an anthracycline antibiotic. The full chemical name ofdoxorubicin is(8S-cis)-10-[(3-amino-2,3,6-trideoxy-α-L-lyxo-hexapyranosyl)oxy]-7,8,9,10-tetrahydro-6,8,11-trihydroxy-8-(hydroxyacetyl)-1-methoxy-5,12-naphthacenedione.

Compositions of the Invention and Methods of Making Same

This invention encompasses compositions, including pharmaceuticalcompositions, comprising an anti-EphB2 antibody; and polynucleotidescomprising sequences encoding an anti-EphB2 antibody. As used herein,compositions comprise one or more antibodies that bind to EphB2, and/orone or more polynucleotides comprising sequences encoding one or moreantibodies that bind to EphB2. These compositions may further comprisesuitable carriers, such as pharmaceutically acceptable excipientsincluding buffers, which are well known in the art.

The invention also encompasses isolated antibody and polynucleotideembodiments. The invention also encompasses substantially pure antibodyand polynucleotide embodiments.

The anti-EphB2 antibodies of the invention are preferably monoclonal.Also encompassed within the scope of the invention are Fab, Fab′,Fab′-SH and F(ab′)₂ fragments of the anti-EphB2 antibodies providedherein. These antibody fragments can be created by traditional means,such as enzymatic digestion, or may be generated by recombinanttechniques. Such antibody fragments may be chimeric or humanized. Thesefragments are useful for the diagnostic and therapeutic purposes setforth below.

Monoclonal antibodies are obtained from a population of substantiallyhomogeneous antibodies, i.e., the individual antibodies comprising thepopulation are identical except for possible naturally occurringmutations that may be present in minor amounts. Thus, the modifier“monoclonal” indicates the character of the antibody as not being amixture of discrete antibodies.

The anti-EphB2 monoclonal antibodies of the invention can be made usingthe hybridoma method first described by Kohler et al., Nature, 256:495(1975), or may be made by recombinant DNA methods (e.g., U.S. Pat. No.4,816,567).

In the hybridoma method, a mouse or other appropriate host animal, suchas a hamster, is immunized to elicit lymphocytes that produce or arecapable of producing antibodies that will specifically bind to theprotein used for immunization. Antibodies to EphB2 generally are raisedin animals by multiple subcutaneous (sc) or intraperitoneal (ip)injections of EphB2 and an adjuvant. EphB2 may be prepared using methodswell-known in the art, some of which are further described herein. Forexample, recombinant production of EphB2 is described below. In oneembodiment, animals are immunized with a derivative of EphB2 thatcontains the extracellular domain (ECD) of EphB2 fused to the Fc portionof an immunoglobulin heavy chain. In a preferred embodiment, animals areimmunized with an EphB2-IgG1 fusion protein. Animals ordinarily areimmunized against immunogenic conjugates or derivatives of EphB2 withmonophosphoryl lipid A (MPL)/trehalose dicrynomycolate (TDM) (RibiImmunochem. Research, Inc., Hamilton, Mont.) and the solution isinjected intradermally at multiple sites. Two weeks later the animalsare boosted. 7 to 14 days later animals are bled and the serum isassayed for anti-EphB2 titer. Animals are boosted until titer plateaus.

Alternatively, lymphocytes may be immunized in vitro. Lymphocytes thenare fused with myeloma cells using a suitable fusing agent, such aspolyethylene glycol, to form a hybridoma cell (Goding, MonoclonalAntibodies: Principles and Practice, pp. 59-103 (Academic Press, 1986)).

The hybridoma cells thus prepared are seeded and grown in a suitableculture medium that preferably contains one or more substances thatinhibit the growth or survival of the unfused, parental myeloma cells.For example, if the parental myeloma cells lack the enzyme hypoxanthineguanine phosphoribosyl transferase (HGPRT or HPRT), the culture mediumfor the hybridomas typically will include hypoxanthine, aminopterin, andthymidine (HAT medium), which substances prevent the growth ofHGPRT-deficient cells.

Preferred myeloma cells are those that fuse efficiently, support stablehigh-level production of antibody by the selected antibody-producingcells, and are sensitive to a medium such as HAT medium. Among these,preferred myeloma cell lines are murine myeloma lines, such as thosederived from MOPC-21 and MPC-11 mouse tumors available from the SalkInstitute Cell Distribution Center, San Diego, Calif. USA, and SP-2 orX63-Ag8-653 cells available from the American Type Culture Collection,Rockville, Md. USA. Human myeloma and mouse-human heteromyeloma celllines also have been described for the production of human monoclonalantibodies (Kozbor, J. Immuunol., 133:3001 (1984); Brodeur et al.,Monoclonal Antibody Production Techniques and Applications, pp. 51-63(Marcel Dekker, Inc., New York, 1987)).

Culture medium in which hybridoma cells are growing is assayed forproduction of monoclonal antibodies directed against EphB2. Preferably,the binding specificity of monoclonal antibodies produced by hybridomacells is determined by immunoprecipitation or by an in vitro bindingassay, such as radioimmunoassay (RIA) or enzyme-linked immunoadsorbentassay (ELISA).

The binding affinity of the monoclonal antibody can, for example, bedetermined by the Scatchard analysis of Munson et al., Anal. Biochem.,107:220 (1980).

After hybridoma cells are identified that produce antibodies of thedesired specificity, affinity, and/or activity, the clones may besubcloned by limiting dilution procedures and grown by standard methods(Goding, Monoclonal Antibodies: Principles and Practice, pp. 59-103(Academic Press, 1986)). Suitable culture media for this purposeinclude, for example, D-MEM or RPMI-1640 medium. In addition, thehybridoma cells may be grown in vivo as ascites tumors in an animal.

The monoclonal antibodies secreted by the subclones are suitablyseparated from the culture medium, ascites fluid, or serum byconventional immunoglobulin purification procedures such as, forexample, protein A-Sepharose, hydroxylapatite chromatography, gelelectrophoresis, dialysis, or affinity chromatography.

The anti-EphB2 antibodies of the invention can be made by usingcombinatorial libraries to screen for synthetic antibody clones with thedesired activity or activities. In principle, synthetic antibody clonesare selected by screening phage libraries containing phage that displayvarious fragments of antibody variable region (Fv) fused to phage coatprotein. Such phage libraries are panned by affinity chromatographyagainst the desired antigen. Clones expressing Fv fragments capable ofbinding to the desired antigen are adsorbed to the antigen and thusseparated from the non-binding clones in the library. The binding clonesare then eluted from the antigen, and can be further enriched byadditional cycles of antigen adsorption/elution. Any of the anti-EphB2antibodies of the invention can be obtained by designing a suitableantigen screening procedure to select for the phage clone of interestfollowed by construction of a full length anti-EphB2 antibody cloneusing the Fv sequences from the phage clone of interest and suitableconstant region (Fc) sequences described in Kabat et al., Sequences ofProteins of Immunological Interest, Fifth Edition, NIH Publication91-3242, Bethesda Md. (1991), vols. 1-3.

The antigen-binding domain of an antibody is formed from two variable(V) regions of about 110 amino acids, one each from the light (VL) andheavy (VH) chains, that both present three hypervariable loops orcomplementarity-determining regions (CDRs). Variable domains can bedisplayed functionally on phage, either as single-chain Fv (scFv)fragments, in which VH and VL are covalently linked through a short,flexible peptide, or as Fab fragments, in which they are each fused to aconstant domain and interact non-covalently, as described in Winter etal, Ann. Rev. Immunol., 12: 433-455 (1994). As used herein, scFvencoding phage clones and Fab encoding phage clones are collectivelyreferred to as “Fv phage clones” or “Fv clones”.

Repertoires of VH and VL genes can be separately cloned by polymerasechain reaction (PCR) and recombined randomly in phage libraries, whichcan then be searched for antigen-binding clones as described in Winteret al, Ann. Rev. Immunol., 12: 433-455 (1994). Libraries from immunizedsources provide high-affinity antibodies to the immunogen without therequirement of constructing hybridomas. Alternatively, the naiverepertoire can be cloned to provide a single source of human antibodiesto a wide range of non-self and also self antigens without anyimmunization as described by Griffiths et al, EMBO J. 12: 725-734(1993). Finally, naive libraries can also be made synthetically bycloning the unrearranged V-gene segments from stem cells, and using PCRprimers containing random sequence to encode the highly variable CDR3regions and to accomplish rearrangement in vitro as described byHoogenboom and Winter, J. Mol. Biol., 227: 381-388 (1992).

Filamentous phage is used to display antibody fragments by fusion to theminor coat protein pIII. The antibody fragments can be displayed assingle chain Fv fragments, in which VH and VL domains are connected onthe same polypeptide chain by a flexible polypeptide spacer, e.g. asdescribed by Marks et al, J. Mol. Biol., 222: 581-597 (1991), or as Fabfragments, in which one chain is fused to pIII and the other is secretedinto the bacterial host cell periplasm where assembly of a Fab-coatprotein structure which becomes displayed on the phage surface bydisplacing some of the wild type coat proteins, e.g. as described inHoogenboom et al, Nucl. Acids Res., 19: 4133-4137 (1991).

In general, nucleic acids encoding antibody gene fragments are obtainedfrom immune cells harvested from humans or animals. If a library biasedin favor of anti-EphB2 clones is desired, the subject is immunized withEphB2 to generate an antibody response, and spleen cells and/orcirculating B cells other peripheral blood lymphocytes (PBLs) arerecovered for library construction. In a preferred embodiment, a humanantibody gene fragment library biased in favor of anti-human EphB2clones is obtained by generating an anti-human EphB2 antibody responsein transgenic mice carrying a functional human immunoglobulin gene array(and lacking a functional endogenous antibody production system) suchthat EphB2 immunization gives rise to B cells producing human antibodiesagainst EphB2. The generation of human antibody-producing transgenicmice is described below.

Additional enrichment for anti-EphB2 reactive cell populations can beobtained by using a suitable screening procedure to isolate B cellsexpressing EphB2-specific membrane bound antibody, e.g., by cellseparation with EphB2 affinity chromatography or adsorption of cells tofluorochrome-labeled EphB2 followed by flow-activated cell sorting(FACS).

Alternatively, the use of spleen cells and/or B cells or other PBLs froman unimmunized donor provides a better representation of the possibleantibody repertoire, and also permits the construction of an antibodylibrary using any animal (human or non-human) species in which EphB2 isnot antigenic. For libraries incorporating in vitro antibody geneconstruction, stem cells are harvested from the subject to providenucleic acids encoding unrearranged antibody gene segments. The immunecells of interest can be obtained from a variety of animal species, suchas human, mouse, rat, lagomorpha, luprine, canine, feline, porcine,bovine, equine, and avian species, etc.

Nucleic acid encoding antibody variable gene segments (including VH andVL segments) are recovered from the cells of interest and amplified. Inthe case of rearranged VH and VL gene libraries, the desired DNA can beobtained by isolating genomic DNA or mRNA from lymphocytes followed bypolymerase chain reaction (PCR) with primers matching the 5′ and 3′ endsof rearranged VH and VL genes as described in Orlandi et al., Proc.Natl. Acad. Sci. (USA), 86: 3833-3837 (1989), thereby making diverse Vgene repertoires for expression. The V genes can be amplified from cDNAand genomic DNA, with back primers at the 5′ end of the exon encodingthe mature V-domain and forward primers based within the J-segment asdescribed in Orlandi et al. (1989) and in Ward et al., Nature, 341:544-546 (1989). However, for amplifying from cDNA, back primers can alsobe based in the leader exon as described in Jones et al., Biotechnol.,9: 88-89 (1991), and forward primers within the constant region asdescribed in Sastry et al., Proc. Natl. Acad. Sci. (USA), 86: 5728-5732(1989). To maximize complementarity, degeneracy can be incorporated inthe primers as described in Orlandi et al. (1989) or Sastry et al.(1989). Preferably, the library diversity is maximized by using PCRprimers targeted to each V-gene family in order to amplify all availableVH and VL arrangements present in the immune cell nucleic acid sample,e.g. as described in the method of Marks et al., J. Mol. Biol., 222:581-597 (1991) or as described in the method of Orum et al., NucleicAcids Res., 21: 4491-4498 (1993). For cloning of the amplified DNA intoexpression vectors, rare restriction sites can be introduced within thePCR primer as a tag at one end as described in Orlandi et al. (1989), orby further PCR amplification with a tagged primer as described inClackson et al., Nature, 352: 624-628 (1991).

Repertoires of synthetically rearranged V genes can be derived in vitrofrom V gene segments. Most of the human VH-gene segments have beencloned and sequenced (reported in Tomlinson et al., J. Mol. Biol., 227:776-798 (1992)), and mapped (reported in Matsuda et al., Nature Genet.,3: 88-94 (1993); these cloned segments (including all the majorconformations of the H1 and H2 loop) can be used to generate diverse VHgene repertoires with PCR primers encoding H3 loops of diverse sequenceand length as described in Hoogenboom and Winter, J. Mol. Biol., 227:381-388 (1992). VH repertoires can also be made with all the sequencediversity focused in a long H3 loop of a single length as described inBarbas et al., Proc. Natl. Acad. Sci. USA, 89: 4457-4461 (1992). HumanVκ and Vλ segments have been cloned and sequenced (reported in Williamsand Winter, Eur. J. Immunol., 23: 1456-1461 (1993)) and can be used tomake synthetic light chain repertoires. Synthetic V gene repertoires,based on a range of VH and VL folds, and L3 and H3 lengths, will encodeantibodies of considerable structural diversity. Following amplificationof V-gene encoding DNAs, germline V-gene segments can be rearranged invitro according to the methods of Hoogenboom and Winter, J. Mol. Biol.,227: 381-388 (1992).

Repertoires of antibody fragments can be constructed by combining VH andVL gene repertoires together in several ways. Each repertoire can becreated in different vectors, and the vectors recombined in vitro, e.g.,as described in Hogrefe et al., Gene, 128: 119-126 (1993), or in vivo bycombinatorial infection, e.g., the loxP system described in Waterhouseet al., Nuc. Acids Res., 21: 2265-2266 (1993). The in vivo recombinationapproach exploits the two-chain nature of Fab fragments to overcome thelimit on library size imposed by E. coli transformation efficiency.Naive VH and VL repertoires are cloned separately, one into a phagemidand the other into a phage vector. The two libraries are then combinedby phage infection of phagemid-containing bacteria so that each cellcontains a different combination and the library size is limited only bythe number of cells present (about 10¹² clones). Both vectors contain invivo recombination signals so that the VH and VL genes are recombinedonto a single replicon and are co-packaged into phage virions. Thesehuge libraries provide large numbers of diverse antibodies of goodaffinity (e.g., K_(d) ⁻¹ of about 10⁻⁸ M).

Alternatively, the repertoires may be cloned sequentially into the samevector, e.g. as described in Barbas et al., Proc. Natl. Acad. Sci. USA,88: 7978-7982 (1991), or assembled together by PCR and then cloned, e.g.as described in Clackson et al., Nature, 352: 624-628 (1991). PCRassembly can also be used to join VH and VL DNAs with DNA encoding aflexible peptide spacer to form single chain Fv (scFv) repertoires. Inyet another technique, “in cell PCR assembly” is used to combine VH andVL genes within lymphocytes by PCR and then clone repertoires of linkedgenes as described in Embleton et al., Nucl. Acids Res., 20: 3831-3837(1992).

The antibodies produced by naive libraries (either natural or synthetic)can be of moderate affinity (K_(d) ⁻¹ of about 10⁶ to 10⁷ M⁻¹), butaffinity maturation can also be mimicked in vitro by constructing andreselecting from secondary libraries as described in Winter et al.(1994), supra. For example, mutation can be introduced at random invitro by using error-prone polymerase (reported in Leung et al.,Technique, 1: 11-15 (1989)) in the method of Hawkins et al., J. Mol.Biol., 226: 889-896 (1992) or in the method of Gram et al., Proc. Natl.Acad. Sci. USA, 89: 3576-3580 (1992). Additionally, affinity maturationcan be performed by randomly mutating one or more CDRs, e.g. using PCRwith primers carrying random sequence spanning the CDR of interest, inselected individual Fv clones and screening for higher affinity clones.WO 9607754 (published 14 Mar. 1996) described a method for inducingmutagenesis in a complementarity determining region of an immunoglobulinlight chain to create a library of light chain genes. Another effectiveapproach is to recombine the VH or VL domains selected by phage displaywith repertoires of naturally occurring V domain variants obtained fromunimmunized donors and screen for higher affinity in several rounds ofchain reshuffling as described in Marks et al., Biotechnol., 10: 779-783(1992). This technique allows the production of antibodies and antibodyfragments with affinities in the 10⁻⁹ M range.

Nucleic acid sequence encoding the EphB2 can be designed using the aminoacid sequence of the desired region of EphB2, e.g. the extracellulardomain spanning amino acids 19 to 542 of the amino acid sequence shownin GenBank Accession Nos. NM_(—)017449, or NM_(—)004442, or FIG. 101 ofWO03/000113, and/or the polypeptide comprising amino acids about 19 toabout 208 of the amino acid sequence shown in GenBank Accession Nos.NM_(—)017449, or NM_(—)004442, or FIG. 101 of WO03/000113.Alternatively, the cDNA sequence (or fragments thereof) of GenBankAccession Nos. NM_(—)017449, or NM_(—)004442, or shown in FIG. 23 ofWO03/000113 may be used. Additional EphB2 sequences are furtherdisclosed in, e.g., Annu. Rev. Neurosci. 21:309-345 (1998), Int. Rev.Cytol. 196:177-244 (2000)); WO2003042661; WO200053216; WO2004065576;WO2004020583; WO2003004529 (Page 128-132); and WO200053216. DNAsencoding EphB2 can be prepared by a variety of methods known in the art.These methods include, but are not limited to, chemical synthesis by anyof the methods described in Engels et al., Agnew. Chem. Int. Ed. Engl.,28: 716-734 (1989), such as the triester, phosphite, phosphoramidite andH-phosphonate methods. In one embodiment, codons preferred by theexpression host cell are used in the design of the EphB2 encoding DNA.Alternatively, DNA encoding the EphB2 can be isolated from a genomic orcDNA library.

Following construction of the DNA molecule encoding the EphB2, the DNAmolecule is operably linked to an expression control sequence in anexpression vector, such as a plasmid, wherein the control sequence isrecognized by a host cell transformed with the vector. In general,plasmid vectors contain replication and control sequences which arederived from species compatible with the host cell. The vectorordinarily carries a replication site, as well as sequences which encodeproteins that are capable of providing phenotypic selection intransformed cells. Suitable vectors for expression in prokaryotic andeukaryotic host cells are known in the art and some are furtherdescribed herein. Eukaryotic organisms, such as yeasts, or cells derivedfrom multicellular organisms, such as mammals, may be used.

Optionally, the DNA encoding the EphB2 is operably linked to a secretoryleader sequence resulting in secretion of the expression product by thehost cell into the culture medium. Examples of secretory leadersequences include stII, ecotin, lamB, herpes GD, 1pp, alkalinephosphatase, invertase, and alpha factor. Also suitable for use hereinis the 36 amino acid leader sequence of protein A (Abrahmsen et al.,EMBO J, 4: 3901 (1985)).

Host cells are transfected and preferably transformed with theabove-described expression or cloning vectors of this invention andcultured in conventional nutrient media modified as appropriate forinducing promoters, selecting transformants, or amplifying the genesencoding the desired sequences.

Transfection refers to the taking up of an expression vector by a hostcell whether or not any coding sequences are in fact expressed. Numerousmethods of transfection are known to the ordinarily skilled artisan, forexample, CaPO₄ precipitation and electroporation. Successfultransfection is generally recognized when any indication of theoperation of this vector occurs within the host cell. Methods fortransfection are well known in the art, and some are further describedherein.

Transformation means introducing DNA into an organism so that the DNA isreplicable, either as an extrachromosomal element or by chromosomalintegrant. Depending on the host cell used, transformation is done usingstandard techniques appropriate to such cells. Methods fortransformation are well known in the art, and some are further describedherein.

Prokaryotic host cells used to produce the EphB2 can be cultured asdescribed generally in Sambrook et al., supra.

The mammalian host cells used to produce the EphB2 can be cultured in avariety of media, which is well known in the art and some of which isdescribed herein.

The host cells referred to in this disclosure encompass cells in invitro culture as well as cells that are within a host animal.

Purification of EphB2 may be accomplished using art-recognized methods,some of which are described herein.

The purified EphB2 can be attached to a suitable matrix such as agarosebeads, acrylamide beads, glass beads, cellulose, various acryliccopolymers, hydroxyl methacrylate gels, polyacrylic and polymethacryliccopolymers, nylon, neutral and ionic carriers, and the like, for use inthe affinity chromatographic separation of phage display clones.Attachment of the EphB2 protein to the matrix can be accomplished by themethods described in Methods in Enzymology, vol. 44 (1976). A commonlyemployed technique for attaching protein ligands to polysaccharidematrices, e.g. agarose, dextran or cellulose, involves activation of thecarrier with cyanogen halides and subsequent coupling of the peptideligand's primary aliphatic or aromatic amines to the activated matrix.

Alternatively, EphB2 can be used to coat the wells of adsorption plates,expressed on host cells affixed to adsorption plates or used in cellsorting, or conjugated to biotin for capture with streptavidin-coatedbeads, or used in any other art-known method for panning phage displaylibraries.

The phage library samples are contacted with immobilized EphB2 underconditions suitable for binding of at least a portion of the phageparticles with the adsorbent. Normally, the conditions, including pH,ionic strength, temperature and the like are selected to mimicphysiological conditions. The phages bound to the solid phase are washedand then eluted by acid, e.g. as described in Barbas et al, Proc. Natl.Acad. Sci. USA, 88: 7978-7982 (1991), or by alkali, e.g. as described inMarks et al., J. Mol. Biol., 222: 581-597 (1991), or by EphB2 antigencompetition, e.g. in a procedure similar to the antigen competitionmethod of Clackson et al., Nature, 352: 624-628 (1991). Phages can beenriched 20-1,000-fold in a single round of selection. Moreover, theenriched phages can be grown in bacterial culture and subjected tofurther rounds of selection.

The efficiency of selection depends on many factors, including thekinetics of dissociation during washing, and whether multiple antibodyfragments on a single phage can simultaneously engage with antigen.Antibodies with fast dissociation kinetics (and weak binding affinities)can be retained by use of short washes, multivalent phage display andhigh coating density of antigen in solid phase. The high density notonly stabilizes the phage through multivalent interactions, but favorsrebinding of phage that has dissociated. The selection of antibodieswith slow dissociation kinetics (and good binding affinities) can bepromoted by use of long washes and monovalent phage display as describedin Bass et al., Proteins, 8: 309-314 (1990) and in WO 92/09690, and alow coating density of antigen as described in Marks et al.,Biotechnol., 10: 779-783 (1992).

It is possible to select between phage antibodies of differentaffinities, even with affinities that differ slightly, for EphB2.However, random mutation of a selected antibody (e.g. as performed insome of the affinity maturation techniques described above) is likely togive rise to many mutants, most binding to antigen, and a few withhigher affinity. With limiting EphB2, rare high affinity phage could becompeted out. To retain all the higher affinity mutants, phages can beincubated with excess biotinylated EphB2, but with the biotinylatedEphB2 at a concentration of lower molarity than the target molaraffinity constant for EphB2. The high affinity-binding phages can thenbe captured by streptavidin-coated paramagnetic beads. Such “equilibriumcapture” allows the antibodies to be selected according to theiraffinities of binding, with sensitivity that permits isolation of mutantclones with as little as two-fold higher affinity from a great excess ofphages with lower affinity. Conditions used in washing phages bound to asolid phase can also be manipulated to discriminate on the basis ofdissociation kinetics.

Anti-EphB2 clones may be activity selected. In one embodiment, theinvention provides anti-EphB2 antibodies that block the binding betweenan EphB2 ligand (such as ephrin-B1, ephrin-B2 and/or ephrin-B3) andEphB2, but do not block the binding between an EphB2 ligand and a secondprotein (such as EphB1, EphB3, EphB4, EphB5 and/or EphB6). Fv clonescorresponding to such anti-EphB2 antibodies can be selected by (1)isolating anti-EphB2 clones from a phage library as described in SectionB(I)(2) above, and optionally amplifying the isolated population ofphage clones by growing up the population in a suitable bacterial host;(2) selecting EphB2 and a second protein against which blocking andnon-blocking activity, respectively, is desired; (3) adsorbing theanti-EphB2 phage clones to immobilized EphB2; (4) using an excess of thesecond protein to elute any undesired clones that recognizeEphB2-binding determinants which overlap or are shared with the bindingdeterminants of the second protein; and (5) eluting the clones whichremain adsorbed following step (4). Optionally, clones with the desiredblocking/non-blocking properties can be further enriched by repeatingthe selection procedures described herein one or more times.

DNA encoding the hybridoma-derived monoclonal antibodies or phagedisplay Fv clones of the invention is readily isolated and sequencedusing conventional procedures (e.g. by using oligonucleotide primersdesigned to specifically amplify the heavy and light chain codingregions of interest from hybridoma or phage DNA template). Onceisolated, the DNA can be placed into expression vectors, which are thentransfected into host cells such as E. coli cells, simian COS cells,Chinese hamster ovary (CHO) cells, or myeloma cells that do nototherwise produce immunoglobulin protein, to obtain the synthesis of thedesired monoclonal antibodies in the recombinant host cells. Reviewarticles on recombinant expression in bacteria of antibody-encoding DNAinclude Skerra et al, Curr. Opinion in Immunol., 5: 256 (1993) andPluckthun, Immuno. Revs, 130: 151 (1992).

DNA encoding the Fv clones of the invention can be combined with knownDNA sequences encoding heavy chain and/or light chain constant regions(e.g. the appropriate DNA sequences can be obtained from Kabat et al,supra) to form clones encoding full or partial length heavy and/or lightchains. It will be appreciated that constant regions of any isotype canbe used for this purpose, including IgG, IgM, IgA, IgD, and IgE constantregions, and that such constant regions can be obtained from any humanor animal species. A Fv clone derived from the variable domain DNA ofone animal (such as human) species and then fused to constant region DNAof another animal species to form coding sequence(s) for “hybrid”, fulllength heavy chain and/or light chain is included in the definition of“chimeric” and “hybrid” antibody as used herein. In a preferredembodiment, a Fv clone derived from human variable DNA is fused to humanconstant region DNA to form coding sequence(s) for all human, full orpartial length heavy and/or light chains.

DNA encoding anti-EphB2 antibody derived from a hybridoma of theinvention can also be modified, for example, by substituting the codingsequence for human heavy- and light-chain constant domains in place ofhomologous murine sequences derived from the hybridoma clone (e.g. as inthe method of Morrison et al., Proc. Natl. Acad. Sci. USA, 81: 6851-6855(1984)). DNA encoding a hybridoma or Fv clone-derived antibody orfragment can be further modified by covalently joining to theimmunoglobulin coding sequence all or part of the coding sequence for anon-immunoglobulin polypeptide. In this manner, “chimeric” or “hybrid”antibodies are prepared that have the binding specificity of the Fvclone or hybridoma clone-derived antibodies of the invention.

Antibody Fragments

The present invention encompasses antibody fragments. In certaincircumstances there are advantages of using antibody fragments, ratherthan whole antibodies. The smaller size of the fragments allows forrapid clearance, and may lead to improved access to solid tumors.

Various techniques have been developed for the production of antibodyfragments. Traditionally, these fragments were derived via proteolyticdigestion of intact antibodies (see, e.g., Morimoto et al., Journal ofBiochemical and Biophysical Methods 24:107-117 (1992); and Brennan etal., Science, 229:81 (1985)). However, these fragments can now beproduced directly by recombinant host cells. Fab, Fv and ScFv antibodyfragments can all be expressed in and secreted from E. coli, thusallowing the facile production of large amounts of these fragments.Antibody fragments can be isolated from the antibody phage librariesdiscussed above. Alternatively, Fab′-SH fragments can be directlyrecovered from E. coli and chemically coupled to form F(ab′)₂ fragments(Carter et al., Bio/Technology 10: 163-167 (1992)). According to anotherapproach, F(ab′)₂ fragments can be isolated directly from recombinanthost cell culture. Fab and F(ab′)₂ fragment with increased in vivohalf-life comprising a salvage receptor binding epitope residues aredescribed in U.S. Pat. No. 5,869,046. Other techniques for theproduction of antibody fragments will be apparent to the skilledpractitioner. In other embodiments, the antibody of choice is a singlechain Fv fragment (scFv). See WO 93/16185; U.S. Pat. Nos. 5,571,894; and5,587,458. Fv and sFv are the only species with intact combining sitesthat are devoid of constant regions; thus, they are suitable for reducednonspecific binding during in vivo use. sFv fusion proteins may beconstructed to yield fusion of an effector protein at either the aminoor the carboxy terminus of an sFv. See Antibody Engineering, ed.Borrebaeck, supra. The antibody fragment may also be a “linearantibody”, e.g., as described in U.S. Pat. No. 5,641,870 for example.Such linear antibody fragments may be monospecific or bispecific.

Humanized Antibodies

The present invention encompasses humanized antibodies. Various methodsfor humanizing non-human antibodies are known in the art. For example, ahumanized antibody can have one or more amino acid residues introducedinto it from a source which is non-human. These non-human amino acidresidues are often referred to as “import” residues, which are typicallytaken from an “import” variable domain. Humanization can be essentiallyperformed following the method of Winter and co-workers (Jones et al.(1986) Nature 321:522-525; Riechmann et al. (1988) Nature 332:323-327;Verhoeyen et al. (1988) Science 239:1534-1536), by substitutinghypervariable region sequences for the corresponding sequences of ahuman antibody. Accordingly, such “humanized” antibodies are chimericantibodies (U.S. Pat. No. 4,816,567) wherein substantially less than anintact human variable domain has been substituted by the correspondingsequence from a non-human species. In practice, humanized antibodies aretypically human antibodies in which some hypervariable region residuesand possibly some FR residues are substituted by residues from analogoussites in rodent antibodies.

The choice of human variable domains, both light and heavy, to be usedin making the humanized antibodies is very important to reduceantigenicity. According to the so-called “best-fit” method, the sequenceof the variable domain of a rodent antibody is screened against theentire library of known human variable-domain sequences. The humansequence which is closest to that of the rodent is then accepted as thehuman framework for the humanized antibody (Sims et al. (1993) J.Immunol. 151:2296; Chothia et al. (1987) J. Mol. Biol. 196:901. Anothermethod uses a particular framework derived from the consensus sequenceof all human antibodies of a particular subgroup of light or heavychains. The same framework may be used for several different humanizedantibodies (Carter et al. (1992) Proc. Natl. Acad. Sci. USA, 89:4285;Presta et al. (1993) J. Immunol., 151:2623.

It is further important that antibodies be humanized with retention ofhigh affinity for the antigen and other favorable biological properties.To achieve this goal, according to one method, humanized antibodies areprepared by a process of analysis of the parental sequences and variousconceptual humanized products using three-dimensional models of theparental and humanized sequences. Three-dimensional immunoglobulinmodels are commonly available and are familiar to those skilled in theart. Computer programs are available which illustrate and displayprobable three-dimensional conformational structures of selectedcandidate immunoglobulin sequences. Inspection of these displays permitsanalysis of the likely role of the residues in the functioning of thecandidate immunoglobulin sequence, i.e., the analysis of residues thatinfluence the ability of the candidate immunoglobulin to bind itsantigen. In this way, FR residues can be selected and combined from therecipient and import sequences so that the desired antibodycharacteristic, such as increased affinity for the target antigen(s), isachieved. In general, the hypervariable region residues are directly andmost substantially involved in influencing antigen binding.

Human Antibodies

Human anti-EphB2 antibodies of the invention can be constructed bycombining Fv clone variable domain sequence(s) selected fromhuman-derived phage display libraries with known human constant domainsequences(s) as described above. Alternatively, human monoclonalanti-EphB2 antibodies of the invention can be made by the hybridomamethod. Human myeloma and mouse-human heteromyeloma cell lines for theproduction of human monoclonal antibodies have been described, forexample, by Kozbor J. Immunol., 133: 3001 (1984); Brodeur et al,Monoclonal Antibody Production Techniques and Applications, pp. 51-63(Marcel Dekker, Inc., New York, 1987); and Boerner et al., J. Immunol.,147: 86 (1991).

It is now possible to produce transgenic animals (e.g. mice) that arecapable, upon immunization, of producing a full repertoire of humanantibodies in the absence of endogenous immunoglobulin production. Forexample, it has been described that the homozygous deletion of theantibody heavy-chain joining region (JH) gene in chimeric and germ-linemutant mice results in complete inhibition of endogenous antibodyproduction. Transfer of the human germ-line immunoglobulin gene array insuch germ-line mutant mice will result in the production of humanantibodies upon antigen challenge. See, e.g., Jakobovits et al, Proc.Natl. Acad. Sci. USA, 90: 2551 (1993); Jakobovits et al., Nature, 362:255 (1993); Bruggermann et al, Year in Immunol., 7: 33 (1993).

Gene shuffling can also be used to derive human antibodies fromnon-human, e.g. rodent, antibodies, where the human antibody has similaraffinities and specificities to the starting non-human antibody.According to this method, which is also called “epitope imprinting”,either the heavy or light chain variable region of a non-human antibodyfragment obtained by phage display techniques as described above isreplaced with a repertoire of human V domain genes, creating apopulation of non-human chain/human chain scFv or Fab chimeras.Selection with antigen results in isolation of a non-human chain/humanchain chimeric scFv or Fab wherein the human chain restores the antigenbinding site destroyed upon removal of the corresponding non-human chainin the primary phage display clone, i.e. the epitope governs (imprints)the choice of the human chain partner. When the process is repeated inorder to replace the remaining non-human chain, a human antibody isobtained (see PCT WO 93/06213 published Apr. 1, 1993). Unliketraditional humanization of non-human antibodies by CDR grafting, thistechnique provides completely human antibodies, which have no FR or CDRresidues of non-human origin.

Bispecific Antibodies

Bispecific antibodies are monoclonal, preferably human or humanized,antibodies that have binding specificities for at least two differentantigens. In the present case, one of the binding specificities is forEphB2 and the other is for any other antigen. Exemplary bispecificantibodies may bind to two different epitopes of the EphB2 protein.Bispecific antibodies may also be used to localize cytotoxic agents tocells which express EphB2. These antibodies possess an EphB2-binding armand an arm which binds the cytotoxic agent (e.g. saporin,anti-interferon-α, vinca alkaloid, ricin A chain, methotrexate orradioactive isotope hapten). Bispecific antibodies can be prepared asfull length antibodies or antibody fragments (e.g. F(ab′)₂ bispecificantibodies).

Methods for making bispecific antibodies are known in the art.Traditionally, the recombinant production of bispecific antibodies isbased on the co-expression of two immunoglobulin heavy chain-light chainpairs, where the two heavy chains have different specificities (Milsteinand Cuello, Nature, 305: 537 (1983)). Because of the random assortmentof immunoglobulin heavy and light chains, these hybridomas (quadromas)produce a potential mixture of 10 different antibody molecules, of whichonly one has the correct bispecific structure. The purification of thecorrect molecule, which is usually done by affinity chromatographysteps, is rather cumbersome, and the product yields are low. Similarprocedures are disclosed in WO 93/08829 published May 13, 1993, and inTraunecker et al, EMBO J., 10: 3655 (1991).

According to a different and more preferred approach, antibody variabledomains with the desired binding specificities (antibody-antigencombining sites) are fused to immunoglobulin constant domain sequences.The fusion preferably is with an immunoglobulin heavy chain constantdomain, comprising at least part of the hinge, CH2, and CH3 regions. Itis preferred to have the first heavy-chain constant region (CHI),containing the site necessary for light chain binding, present in atleast one of the fusions. DNAs encoding the immunoglobulin heavy chainfusions and, if desired, the immunoglobulin light chain, are insertedinto separate expression vectors, and are co-transfected into a suitablehost organism. This provides for great flexibility in adjusting themutual proportions of the three polypeptide fragments in embodimentswhen unequal ratios of the three polypeptide chains used in theconstruction provide the optimum yields. It is, however, possible toinsert the coding sequences for two or all three polypeptide chains inone expression vector when the expression of at least two polypeptidechains in equal ratios results in high yields or when the ratios are ofno particular significance.

In a preferred embodiment of this approach, the bispecific antibodiesare composed of a hybrid immunoglobulin heavy chain with a first bindingspecificity in one arm, and a hybrid immunoglobulin heavy chain-lightchain pair (providing a second binding specificity) in the other arm. Itwas found that this asymmetric structure facilitates the separation ofthe desired bispecific compound from unwanted immunoglobulin chaincombinations, as the presence of an immunoglobulin light chain in onlyone half of the bispecific molecule provides for a facile way ofseparation. This approach is disclosed in WO 94/04690. For furtherdetails of generating bispecific antibodies see, for example, Suresh etal, Methods in Enzymology, 121:210 (1986).

According to another approach, the interface between a pair of antibodymolecules can be engineered to maximize the percentage of heterodimerswhich are recovered from recombinant cell culture. The preferredinterface comprises at least a part of the C_(H)3 domain of an antibodyconstant domain. In this method, one or more small amino acid sidechains from the interface of the first antibody molecule are replacedwith larger side chains (e.g. tyrosine or tryptophan). Compensatory“cavities” of identical or similar size to the large side chain(s) arecreated on the interface of the second antibody molecule by replacinglarge amino acid side chains with smaller ones (e.g. alanine orthreonine). This provides a mechanism for increasing the yield of theheterodimer over other unwanted end-products such as homodimers.

Bispecific antibodies include cross-linked or “heteroconjugate”antibodies. For example, one of the antibodies in the heteroconjugatecan be coupled to avidin, the other to biotin. Such antibodies have, forexample, been proposed to target immune system cells to unwanted cells(U.S. Pat. No. 4,676,980), and for treatment of HIV infection (WO91/00360, WO 92/00373, and EP 03089). Heteroconjugate antibodies may bemade using any convenient cross-linking methods. Suitable cross-linkingagents are well known in the art, and are disclosed in U.S. Pat. No.4,676,980, along with a number of cross-linking techniques.

Techniques for generating bispecific antibodies from antibody fragmentshave also been described in the literature. For example, bispecificantibodies can be prepared using chemical linkage. Brennan et al,Science, 229: 81 (1985) describe a procedure wherein intact antibodiesare proteolytically cleaved to generate F(ab′)₂ fragments. Thesefragments are reduced in the presence of the dithiol complexing agentsodium arsenite to stabilize vicinal dithiols and prevent intermoleculardisulfide formation. The Fab′ fragments generated are then converted tothionitrobenzoate (TNB) derivatives. One of the Fab′-TNB derivatives isthen reconverted to the Fab′-thiol by reduction with mercaptoethylamineand is mixed with an equimolar amount of the other Fab′-TNB derivativeto form the bispecific antibody. The bispecific antibodies produced canbe used as agents for the selective immobilization of enzymes.

Recent progress has facilitated the direct recovery of Fab′-SH fragmentsfrom E. coli, which can be chemically coupled to form bispecificantibodies. Shalaby et al, J. Exp. Med., 175: 217-225 (1992) describethe production of a fully humanized bispecific antibody F(ab′)₂molecule. Each Fab′ fragment was separately secreted from E. coli andsubjected to directed chemical coupling in vitro to form the bispecificantibody. The bispecific antibody thus formed was able to bind to cellsoverexpressing the HER2 receptor and normal human T cells, as well astrigger the lytic activity of human cytotoxic lymphocytes against humanbreast tumor targets.

Various techniques for making and isolating bispecific antibodyfragments directly from recombinant cell culture have also beendescribed. For example, bispecific antibodies have been produced usingleucine zippers. Kostelny et al, J. Immunol., 148(5):1547-1553 (1992).The leucine zipper peptides from the Fos and Jun proteins were linked tothe Fab′ portions of two different antibodies by gene fusion. Theantibody homodimers were reduced at the hinge region to form monomersand then re-oxidized to form the antibody heterodimers. This method canalso be utilized for the production of antibody homodimers. The“diabody” technology described by Hollinger et al., Proc. Natl. Acad.Sci. USA, 90:6444-6448 (1993) has provided an alternative mechanism formaking bispecific antibody fragments. The fragments comprise aheavy-chain variable domain (VH) connected to a light-chain variabledomain (VL) by a linker which is too short to allow pairing between thetwo domains on the same chain. Accordingly, the VH and VL domains of onefragment are forced to pair with the complementary VL and VH domains ofanother fragment, thereby forming two antigen-binding sites. Anotherstrategy for making bispecific antibody fragments by the use ofsingle-chain Fv (sFv) dimers has also been reported. See Gruber et al.,J. Immunol., 152:5368 (1994).

Antibodies with more than two valencies are contemplated. For example,trispecific antibodies can be prepared. Tutt et al. J. Immunol. 147: 60(1991).

Multivalent Antibodies

A multivalent antibody may be internalized (and/or catabolized) fasterthan a bivalent antibody by a cell expressing an antigen to which theantibodies bind. The antibodies of the present invention can bemultivalent antibodies (which are other than of the IgM class) withthree or more antigen binding sites (e.g. tetravalent antibodies), whichcan be readily produced by recombinant expression of nucleic acidencoding the polypeptide chains of the antibody. The multivalentantibody can comprise a dimerization domain and three or more antigenbinding sites. The preferred dimerization domain comprises (or consistsof) an Fc region or a hinge region. In this scenario, the antibody willcomprise an Fc region and three or more antigen binding sitesamino-terminal to the Fe region. The preferred multivalent antibodyherein comprises (or consists of) three to about eight, but preferablyfour, antigen binding sites. The multivalent antibody comprises at leastone polypeptide chain (and preferably two polypeptide chains), whereinthe polypeptide chain(s) comprise two or more variable domains. Forinstance, the polypeptide chain(s) may comprise VD1-(X1)n-VD2-(X2)n-Fc,wherein VD1 is a first variable domain, VD2 is a second variable domain,Fc is one polypeptide chain of an Fc region, X1 and X2 represent anamino acid or polypeptide, and n is 0 or 1. For instance, thepolypeptide chain(s) may comprise: VH-CH1-flexible linker-VH-CH1-Fcregion chain; or VH-CH1-VH-CH1-Fc region chain. The multivalent antibodyherein preferably further comprises at least two (and preferably four)light chain variable domain polypeptides. The multivalent antibodyherein may, for instance, comprise from about two to about eight lightchain variable domain polypeptides. The light chain variable domainpolypeptides contemplated here comprise a light chain variable domainand, optionally, further comprise a CL domain.

Antibody Variants

In some embodiments, amino acid sequence modification(s) of theantibodies described herein are contemplated. For example, it may bedesirable to improve the binding affinity and/or other biologicalproperties of the antibody. Amino acid sequence variants of the antibodyare prepared by introducing appropriate nucleotide changes into theantibody nucleic acid, or by peptide synthesis. Such modificationsinclude, for example, deletions from, and/or insertions into and/orsubstitutions of, residues within the amino acid sequences of theantibody. Any combination of deletion, insertion, and substitution ismade to arrive at the final construct, provided that the final constructpossesses the desired characteristics. The amino acid alterations may beintroduced in the subject antibody amino acid sequence at the time thatsequence is made.

A useful method for identification of certain residues or regions of theantibody that are preferred locations for mutagenesis is called “alaninescanning mutagenesis” as described by Cunningham and Wells (1989)Science, 244:1081-1085. Here, a residue or group of target residues areidentified (e.g., charged residues such as arg, asp, his, lys, and glu)and replaced by a neutral or negatively charged amino acid (mostpreferably alanine or polyalanine) to affect the interaction of theamino acids with antigen. Those amino acid locations demonstratingfunctional sensitivity to the substitutions then are refined byintroducing further or other variants at, or for, the sites ofsubstitution. Thus, while the site for introducing an amino acidsequence variation is predetermined, the nature of the mutation per seneed not be predetermined. For example, to analyze the performance of amutation at a given site, ala scanning or random mutagenesis isconducted at the target codon or region and the expressedimmunoglobulins are screened for the desired activity.

Amino acid sequence insertions include amino- and/or carboxyl-terminalfusions ranging in length from one residue to polypeptides containing ahundred or more residues, as well as intrasequence insertions of singleor multiple amino acid residues. Examples of terminal insertions includean antibody with an N-terminal methionyl residue or the antibody fusedto a cytotoxic polypeptide. Other insertional variants of the antibodymolecule include the fusion to the N- or C-terminus of the antibody toan enzyme (e.g. for ADEPT) or a polypeptide which increases the serumhalf-life of the antibody.

Glycosylation of polypeptides is typically either N-linked or O-linked.N-linked refers to the attachment of the carbohydrate moiety to the sidechain of an asparagine residue. The tripeptide sequencesasparagine-X-serine and asparagine-X-threonine, where X is any aminoacid except proline, are the recognition sequences for enzymaticattachment of the carbohydrate moiety to the asparagine side chain.Thus, the presence of either of these tripeptide sequences in apolypeptide creates a potential glycosylation site. O-linkedglycosylation refers to the attachment of one of the sugarsN-aceylgalactosamine, galactose, or xylose to a hydroxyamino acid, mostcommonly serine or threonine, although 5-hydroxyproline or5-hydroxylysine may also be used.

Addition of glycosylation sites to the antibody is convenientlyaccomplished by altering the amino acid sequence such that it containsone or more of the above-described tripeptide sequences (for N-linkedglycosylation sites). The alteration may also be made by the additionof, or substitution by, one or more serine or threonine residues to thesequence of the original antibody (for O-linked glycosylation sites).

Where the antibody comprises an Fc region, the carbohydrate attachedthereto may be altered. For example, antibodies with a maturecarbohydrate structure that lacks fucose attached to an Fc region of theantibody are described in US Pat Appl No US 2003/0157108 (Presta, L.).See also US 2004/0093621 (Kyowa Hakko Kogyo Co., Ltd). Antibodies with abisecting N-acetylglucosamine (GlcNAc) in the carbohydrate attached toan Fc region of the antibody are referenced in WO 2003/011878,Jean-Mairet et al. and U.S. Pat. No. 6,602,684, Umana et al. Antibodieswith at least one galactose residue in the oligosaccharide attached toan Fc region of the antibody are reported in WO 1997/30087, Patel et al.See, also, WO 1998/58964 (Raju, S.) and WO 1999/22764 (Raju, S.)concerning antibodies with altered carbohydrate attached to the Fcregion thereof. See also US 2005/0123546 (Umana et al.) onantigen-binding molecules with modified glycosylation.

The preferred glycosylation variant herein comprises an Fc region,wherein a carbohydrate structure attached to the Fc region lacks fucose.Such variants have improved ADCC function. Optionally, the Fc regionfurther comprises one or more amino acid substitutions therein whichfurther improve ADCC, for example, substitutions at positions 298, 333,and/or 334 of the Fc region (Eu numbering of residues). Examples ofpublications related to “defucosylated” or “fucose-deficient” antibodiesinclude: US 2003/0157108; WO 2000/61739; WO 2001/29246; US 2003/0115614;US 2002/0164328; US 2004/0093621; US 2004/0132140; US 2004/0110704; US2004/0110282; US 2004/0109865; WO 2003/085119; WO 2003/084570; WO2005/035586; WO 2005/035778; WO2005/053742; Okazaki et al. J. Mol. Biol.336:1239-1249 (2004); Yamane-Ohnuki et al. Biotech. Bioeng. 87: 614(2004). Examples of cell lines producing defucosylated antibodiesinclude Lec 13 CHO cells deficient in protein fucosylation (Ripka et al.Arch. Biochem. Biophys. 249:533-545 (1986); US Pat Appl No US2003/0157108 A1, Presta, L; and WO 2004/056312 A1, Adams et al.,especially at Example 11), and knockout cell lines, such asalpha-1,6-fucosyltransferase gene, FUT8, knockout CHO cells(Yamane-Ohnuki et al. Biotech. Bioeng. 87: 614 (2004)).

Another type of variant is an amino acid substitution variant. Thesevariants have at least one amino acid residue in the antibody moleculereplaced by a different residue. The sites of greatest interest forsubstitutional mutagenesis include the hypervariable regions, but FRalterations are also contemplated. Conservative substitutions are shownin Table 1 under the heading of “preferred substitutions”. If suchsubstitutions result in a change in biological activity, then moresubstantial changes, denominated “exemplary substitutions” in Table 1,or as further described below in reference to amino acid classes, may beintroduced and the products screened.

TABLE 1 Original Exemplary Preferred Residue Substitutions SubstitutionsAla (A) Val; Leu; Ile Val Arg (R) Lys; Gln; Asn Lys Asn (N) Gln; His;Asp, Lys; Arg Gln Asp (D) Glu; Asn Glu Cys (C) Ser; Ala Ser Gln (Q) Asn;Glu Asn Glu (E) Asp; Gln Asp Gly (G) Ala Ala His (H) Asn; Gln; Lys; ArgArg Ile (I) Leu; Val; Met; Ala; Leu Phe; Norleucine Leu (L) Norleucine;Ile; Val; Ile Met; Ala; Phe Lys (K) Arg; Gln; Asn Arg Met (M) Leu; Phe;Ile Leu Phe (F) Trp; Leu; Val; Ile; Ala; Tyr Tyr Pro (P) Ala Ala Ser (S)Thr Thr Thr (T) Val; Ser Ser Trp (W) Tyr; Phe Tyr Tyr (Y) Trp; Phe; Thr;Ser Phe Val (V) Ile; Leu; Met; Phe; Leu Ala; Norleucine

Substantial modifications in the biological properties of the antibodyare accomplished by selecting substitutions that differ significantly intheir effect on maintaining (a) the structure of the polypeptidebackbone in the area of the substitution, for example, as a sheet orhelical conformation, (b) the charge or hydrophobicity of the moleculeat the target site, or (c) the bulk of the side chain. Naturallyoccurring residues are divided into groups based on common side-chainproperties:

-   -   (1) hydrophobic: norleucine, met, ala, val, leu, ile;    -   (2) neutral hydrophilic: Cys, Ser, Thr, Asn, Gln;    -   (3) acidic: asp, glu;    -   (4) basic: his, lys, arg;    -   (5) residues that influence chain orientation: gly, pro; and    -   (6) aromatic: trp, tyr, phe.

Non-conservative substitutions will entail exchanging a member of one ofthese classes for another class.

One type of substitutional variant involves substituting one or morehypervariable region residues of a parent antibody (e.g. a humanized orhuman antibody). Generally, the resulting variant(s) selected forfurther development will have improved biological properties relative tothe parent antibody from which they are generated. A convenient way forgenerating such substitutional variants involves affinity maturationusing phage display. Briefly, several hypervariable region sites (e.g.6-7 sites) are mutated to generate all possible amino acid substitutionsat each site. The antibodies thus generated are displayed fromfilamentous phage particles as fusions to the gene III product of M13packaged within each particle. The phage-displayed variants are thenscreened for their biological activity (e.g. binding affinity) as hereindisclosed. In order to identify candidate hypervariable region sites formodification, alanine scanning mutagenesis can be performed to identifyhypervariable region residues contributing significantly to antigenbinding. Alternatively, or additionally, it may be beneficial to analyzea crystal structure of the antigen-antibody complex to identify contactpoints between the antibody and antigen. Such contact residues andneighboring residues are candidates for substitution according to thetechniques elaborated herein. Once such variants are generated, thepanel of variants is subjected to screening as described herein andantibodies with superior properties in one or more relevant assays maybe selected for further development.

Nucleic acid molecules encoding amino acid sequence variants of theantibody are prepared by a variety of methods known in the art. Thesemethods include, but are not limited to, isolation from a natural source(in the case of naturally occurring amino acid sequence variants) orpreparation by oligonucleotide-mediated (or site-directed) mutagenesis,PCR mutagenesis, and cassette mutagenesis of an earlier prepared variantor a non-variant version of the antibody.

It may be desirable to introduce one or more amino acid modifications inan Fc region of the immunoglobulin polypeptides of the invention,thereby generating a Fc region variant. The Fc region variant maycomprise a human Fc region sequence (e.g., a human IgG1, IgG2, IgG3 orIgG4 Fc region) comprising an amino acid modification (e.g. asubstitution) at one or more amino acid positions including that of ahinge cysteine.

In accordance with this description and the teachings of the art, it iscontemplated that in some embodiments, an antibody used in methods ofthe invention may comprise one or more alterations as compared to thewild type counterpart antibody, e.g. in the Fc region. These antibodieswould nonetheless retain substantially the same characteristics requiredfor therapeutic utility as compared to their wild type counterpart. Forexample, it is thought that certain alterations can be made in the Fcregion that would result in altered (i.e., either improved ordiminished) C1q binding and/or Complement Dependent Cytotoxicity (CDC),e.g., as described in WO99/51642. See also Duncan & Winter Nature322:738-40 (1988); U.S. Pat. No. 5,648,260; U.S. Pat. No. 5,624,821; andWO94/29351 concerning other examples of Fc region variants. WO00/42072(Presta) and WO 2004/056312 (Lowman) describe antibody variants withimproved or diminished binding to FcRs. The content of these patentpublications are specifically incorporated herein by reference. See,also, Shields et al. J. Biol. Chem. 9(2): 6591-6604 (2001). Antibodieswith increased half lives and improved binding to the neonatal Fcreceptor (FcRn), which is responsible for the transfer of maternal IgGsto the fetus (Guyer et al., J. Immunol. 117:587 (1976) and Kim et al.,J. Immunol. 24:249 (1994)), are described in US2005/0014934A1 (Hinton etal.). These antibodies comprise an Fc region with one or moresubstitutions therein which improve binding of the Fc region to FcRn.Polypeptide variants with altered Fc region amino acid sequences andincreased or decreased C1q binding capability are described in U.S. Pat.No. 6,194,551B1, WO99/51642. The contents of those patent publicationsare specifically incorporated herein by reference. See, also, Idusogieet al. J. Immunol. 164:4178-4184 (2000).

Antibody Derivatives

The antibodies of the present invention can be further modified tocontain additional nonproteinaceous moieties that are known in the artand readily available. Preferably, the moieties suitable forderivatization of the antibody are water soluble polymers. Non-limitingexamples of water soluble polymers include, but are not limited to,polyethylene glycol (PEG), copolymers of ethylene glycol/propyleneglycol, carboxymethylcellulose, dextran, polyvinyl alcohol, polyvinylpyrrolidone, poly-1,3-dioxolane, poly-1,3,6-trioxane, ethylene/maleicanhydride copolymer, polyaminoacids (either homopolymers or randomcopolymers), and dextran or poly(n-vinyl pyrrolidone)polyethyleneglycol, propropylene glycol homopolymers, prolypropylene oxide/ethyleneoxide co-polymers, polyoxyethylated polyols (e.g., glycerol), polyvinylalcohol, and mixtures thereof. Polyethylene glycol propionaldehyde mayhave advantages in manufacturing due to its stability in water. Thepolymer may be of any molecular weight, and may be branched orunbranched. The number of polymers attached to the antibody may vary,and if more than one polymers are attached, they can be the same ordifferent molecules. In general, the number and/or type of polymers usedfor derivatization can be determined based on considerations including,but not limited to, the particular properties or functions of theantibody to be improved, whether the antibody derivative will be used ina therapy under defined conditions, etc.

Screening for Antibodies with Desired Properties

The antibodies of the present invention can be characterized for theirphysical/chemical properties and biological functions by various assaysknown in the art. In some embodiments, antibodies are characterized forany one or more of reduction or blocking of EphB2 activation, reductionor blocking of EphB2 downstream molecular signaling, reduction orblocking of EphB2 ligand activation, reduction or blocking or EphB2ligand downstream molecular signaling, disruption or blocking of ligand(e.g., ephrin-B1, ephrin-B2, and/or ephrin-B3) binding to EphB2, EphB2phosphorylation and/or EphB2 multimerization, and/or EphB2 ligandphosphorylation, and/or treatment and/or prevention of a tumor, cellproliferative disorder or a cancer; and/or treatment or prevention of adisorder associated with EphB2 expression and/or activity (such asincreased EphB2 expression and/or activity).

The purified antibodies can be further characterized by a series ofassays including, but not limited to, N-terminal sequencing, amino acidanalysis, non-denaturing size exclusion high pressure liquidchromatography (HPLC), mass spectrometry, ion exchange chromatographyand papain digestion.

In certain embodiments of the invention, the antibodies produced hereinare analyzed for their biological activity. In some embodiments, theantibodies of the present invention are tested for their antigen bindingactivity. The antigen binding assays that are known in the art and canbe used herein include without limitation any direct or competitivebinding assays using techniques such as western blots,radioimmunoassays, ELISA (enzyme linked immunosorbent assay), “sandwich”immunoassays, immunoprecipitation assays, fluorescent immunoassays, andprotein A immunoassays. Illustrative antigen binding assay are providedbelow in the Examples section.

In another embodiment, the invention provides the anti-EphB2 monoclonalantibody produced by hybridoma cell line 2H9.11.14 (ATCC Deposit No.PTA-6606) (interchangeably termed “2H9” or “Mab 2H9” herein).

In still another embodiment, the invention provides anti-EphB2monoclonal antibodies that compete with 2H9 antibody for binding toEphB2. Such competitor antibodies include antibodies that recognize anEphB2 epitope that is the same as or overlaps with the EphB2 epitoperecognized by antibody 2H9. Such competitor antibodies can be obtainedby screening anti-EphB2 hybridoma supernatants for binding toimmobilized EphB2 in competition with labeled 2H9 antibody. A hybridomasupernatant containing competitor antibody will reduce the amount ofbound, labeled antibody detected in the subject competition bindingmixture as compared to the amount of bound, labeled antibody detected ina control binding mixture containing irrelevant (or no) antibody. Any ofthe competition binding assays described herein are suitable for use inthe foregoing procedure.

In another aspect, the invention provides an anti-EphB2 monoclonalantibody that comprises one or more (such as 2, 3, 4, 5, and/or 6) HVRsof the 2H9 antibody. An anti-EphB2 monoclonal antibody that comprisesone or more HVR(s) of 2H9 can be constructed by grafting one or moreHVR(s) of 2H9 onto a template antibody sequence, e.g. a human antibodysequence which is closest to the corresponding murine sequence of theparental antibody, or a consensus sequence of all human antibodies inthe particular subgroup of the parental antibody light or heavy chain,and expressing the resulting chimeric light and/or heavy chain variableregion sequence(s), with or without accompanying constant regionsequence(s), in recombinant host cells as described herein.

Anti-EphB2 antibodies of the invention possessing the unique propertiesdescribed herein can be obtained by screening anti-EphB2 hybridomaclones for the desired properties by any convenient method. For example,if an anti-EphB2 monoclonal antibody that blocks or does not block thebinding of EphB2 ligands to EphB2 is desired, the candidate antibody canbe tested in a binding competition assay, such as a competitive bindingELISA, wherein plate wells are coated with EphB2, and a solution ofantibody in an excess of the Eph ligand of interest is layered onto thecoated plates, and bound antibody is detected enzymatically, e.g.contacting the bound antibody with HRP-conjugated anti-Ig antibody orbiotinylated anti-Ig antibody and developing the HRP color reaction,e.g. by developing plates with streptavidin-HRP and/or hydrogen peroxideand detecting the HRP color reaction by spectrophotometry at 490 nm withan ELISA plate reader.

If an anti-EphB2 antibody that inhibits EphB2 activation is desired, thecandidate antibody can be tested in an EphB2 phosphorylation assay. Suchassays are known in the art and one such assay is described andexemplified in the Examples section. If an antibody that interferes withantibody internalization is desired, the candidate assay can be testedin a cell internalization assay. Such assays are known in the art andone such assay is described and exemplified in the Examples section.

If an anti-EphB2 antibody or immunoconjugate that kills cells orinhibits cell growth is desired, the candidate antibody orimmunoconjugate can be tested in in vitro and/or in vivo assays thatmeasure cell killing and/or inhibition of cell growth. Such assays areknown in the art and are further described and exemplified herein.

In one embodiment, the present invention contemplates an alteredantibody that possesses some but not all effector functions, which makeit a desired candidate for many applications in which the half life ofthe antibody in vivo is important yet certain effector functions (suchas complement and ADCC) are unnecessary or deleterious. In certainembodiments, the Fc activities of the produced immunoglobulin aremeasured to ensure that only the desired properties are maintained. Invitro and/or in vivo cytotoxicity assays can be conducted to confirm thereduction/depletion of CDC and/or ADCC activities. For example, Fcreceptor (FcR) binding assays can be conducted to ensure that theantibody lacks FcγR binding (hence likely lacking ADCC activity), butretains FcRn binding ability. The primary cells for mediating ADCC, NKcells, express FcγRIII only, whereas monocytes express FcγRI, FcγRII andFcγRIII. FcR expression on hematopoietic cells is summarized in Table 3on page 464 of Ravetch and Kinet, Annu. Rev. Immunol 9:457-92 (1991). Anexample of an in vitro assay to assess ADCC activity of a molecule ofinterest is described in U.S. Pat. No. 5,500,362 or 5,821,337. Usefuleffector cells for such assays include peripheral blood mononuclearcells (PBMC) and Natural Killer (NK) cells. Alternatively, oradditionally, ADCC activity of the molecule of interest may be assessedin vivo, e.g., in a animal model such as that disclosed in Clynes et al.PNAS (USA) 95:652-656 (1998). C1q binding assays may also be carried outto confirm that the antibody is unable to bind C1q and hence lacks CDCactivity. To assess complement activation, a CDC assay, e.g. asdescribed in Gazzano-Santoro et al., J. Immunol. Methods 202:163 (1996),may be performed. FcRn binding and in vivo clearance/half lifedeterminations can also be performed using methods known in the art,e.g. those described in the Examples section.

Vectors, Host Cells and Recombinant Methods

For recombinant production of an antibody of the invention, the nucleicacid encoding it is isolated and inserted into a replicable vector forfurther cloning (amplification of the DNA) or for expression. DNAencoding the antibody is readily isolated and sequenced usingconventional procedures (e.g., by using oligonucleotide probes that arecapable of binding specifically to genes encoding the heavy and lightchains of the antibody). Many vectors are available. The choice ofvector depends in part on the host cell to be used. Generally, preferredhost cells are of either prokaryotic or eukaryotic (generally mammalian)origin. It will be appreciated that constant regions of any isotype canbe used for this purpose, including IgG, IgM, IgA, IgD, and IgE constantregions, and that such constant regions can be obtained from any humanor animal species.

a. Generating Antibodies using Prokaryotic Host Cells:

i. Vector Construction

Polynucleotide sequences encoding polypeptide components of the antibodyof the invention can be obtained using standard recombinant techniques.Desired polynucleotide sequences may be isolated and sequenced fromantibody producing cells such as hybridoma cells. Alternatively,polynucleotides can be synthesized using nucleotide synthesizer or PCRtechniques. Once obtained, sequences encoding the polypeptides areinserted into a recombinant vector capable of replicating and expressingheterologous polynucleotides in prokaryotic hosts. Many vectors that areavailable and known in the art can be used for the purpose of thepresent invention. Selection of an appropriate vector will depend mainlyon the size of the nucleic acids to be inserted into the vector and theparticular host cell to be transformed with the vector. Each vectorcontains various components, depending on its function (amplification orexpression of heterologous polynucleotide, or both) and itscompatibility with the particular host cell in which it resides. Thevector components generally include, but are not limited to: an originof replication, a selection marker gene, a promoter, a ribosome bindingsite (RBS), a signal sequence, the heterologous nucleic acid insert anda transcription termination sequence.

In general, plasmid vectors containing replicon and control sequenceswhich are derived from species compatible with the host cell are used inconnection with these hosts. The vector ordinarily carries a replicationsite, as well as marking sequences which are capable of providingphenotypic selection in transformed cells. For example, E. coli istypically transformed using pBR322, a plasmid derived from an E. colispecies. pBR322 contains genes encoding ampicillin (Amp) andtetracycline (Tet) resistance and thus provides easy means foridentifying transformed cells. pBR322, its derivatives, or othermicrobial plasmids or bacteriophage may also contain, or be modified tocontain, promoters which can be used by the microbial organism forexpression of endogenous proteins. Examples of pBR322 derivatives usedfor expression of particular antibodies are described in detail inCarter et al., U.S. Pat. No. 5,648,237.

In addition, phage vectors containing replicon and control sequencesthat are compatible with the host microorganism can be used astransforming vectors in connection with these hosts. For example,bacteriophage such as λGEM.TM.-11 may be utilized in making arecombinant vector which can be used to transform susceptible host cellssuch as E. coli LE392.

The expression vector of the invention may comprise two or morepromoter-cistron pairs, encoding each of the polypeptide components. Apromoter is an untranslated regulatory sequence located upstream (5′) toa cistron that modulates its expression. Prokaryotic promoters typicallyfall into two classes, inducible and constitutive. Inducible promoter isa promoter that initiates increased levels of transcription of thecistron under its control in response to changes in the culturecondition, e.g. the presence or absence of a nutrient or a change intemperature.

A large number of promoters recognized by a variety of potential hostcells are well known. The selected promoter can be operably linked tocistron DNA encoding the light or heavy chain by removing the promoterfrom the source DNA via restriction enzyme digestion and inserting theisolated promoter sequence into the vector of the invention. Both thenative promoter sequence and many heterologous promoters may be used todirect amplification and/or expression of the target genes. In someembodiments, heterologous promoters are utilized, as they generallypermit greater transcription and higher yields of expressed target geneas compared to the native target polypeptide promoter.

Promoters suitable for use with prokaryotic hosts include the PhoApromoter, the β-galactamase and lactose promoter systems, a tryptophan(trp) promoter system and hybrid promoters such as the tac or the trcpromoter. However, other promoters that are functional in bacteria (suchas other known bacterial or phage promoters) are suitable as well. Theirnucleotide sequences have been published, thereby enabling a skilledworker operably to ligate them to cistrons encoding the target light andheavy chains (Siebenlist et al. (1980) Cell 20: 269) using linkers oradaptors to supply any required restriction sites.

In one aspect of the invention, each cistron within the recombinantvector comprises a secretion signal sequence component that directstranslocation of the expressed polypeptides across a membrane. Ingeneral, the signal sequence may be a component of the vector, or it maybe a part of the target polypeptide DNA that is inserted into thevector. The signal sequence selected for the purpose of this inventionshould be one that is recognized and processed (i.e. cleaved by a signalpeptidase) by the host cell. For prokaryotic host cells that do notrecognize and process the signal sequences native to the heterologouspolypeptides, the signal sequence is substituted by a prokaryotic signalsequence selected, for example, from the group consisting of thealkaline phosphatase, penicillinase, Ipp, or heat-stable enterotoxin II(STII) leaders, LamB, PhoE, PelB, OmpA and MBP. In one embodiment of theinvention, the signal sequences used in both cistrons of the expressionsystem are STII signal sequences or variants thereof.

In another aspect, the production of the immunoglobulins according tothe invention can occur in the cytoplasm of the host cell, and thereforedoes not require the presence of secretion signal sequences within eachcistron. In that regard, immunoglobulin light and heavy chains areexpressed, folded and assembled to form functional immunoglobulinswithin the cytoplasm. Certain host strains (e.g., the E. colitrxB-strains) provide cytoplasm conditions that are favorable fordisulfide bond formation, thereby permitting proper folding and assemblyof expressed protein subunits (Proba and Pluckthun Gene, 159:203(1995)).

Prokaryotic host cells suitable for expressing antibodies of theinvention include Archaebacteria and Eubacteria, such as Gram-negativeor Gram-positive organisms. Examples of useful bacteria includeEscherichia (e.g., E. coli), Bacilli (e.g., B. subtilis),Enterobacteria, Pseudomonas species (e.g., P. aeruginosa), Salmonellatyphimurium, Serratia marcescans, Klebsiella, Proteus, Shigella,Rhizobia, Vitreoscilla, or Paracoccus. In one embodiment, gram-negativecells are used. In one embodiment, E. coli cells are used as hosts forthe invention. Examples of E. coli strains include strain W3110(Bachmann, Cellular and Molecular Biology, vol. 2 (Washington, D.C.:American Society for Microbiology, 1987), pp. 1190-1219; ATCC DepositNo. 27,325) and derivatives thereof, including strain 33D3 havinggenotype W3110 ΔfhuA (ΔtonA) ptr3 lac Iq lacL8 ΔompTΔ(nmpc-fepE) degP41kanR (U.S. Pat. No. 5,639,635). Other strains and derivatives thereof,such as E. coli 294 (ATCC 31,446), E. coli B, E. coliλ1776 (ATCC 31,537)and E. coli RV308(ATCC 31,608) are also suitable. These examples areillustrative rather than limiting. Methods for constructing derivativesof any of the above-mentioned bacteria having defined genotypes areknown in the art and described in, for example, Bass et al., Proteins,8:309-314 (1990). It is generally necessary to select the appropriatebacteria taking into consideration replicability of the replicon in thecells of a bacterium. For example, E. coli, Serratia, or Salmonellaspecies can be suitably used as the host when well known plasmids suchas pBR322, pBR325, pACYC177, or pKN410 are used to supply the replicon.Typically the host cell should secrete minimal amounts of proteolyticenzymes, and additional protease inhibitors may desirably beincorporated in the cell culture.

ii. Antibody Production

Host cells are transformed with the above-described expression vectorsand cultured in conventional nutrient media modified as appropriate forinducing promoters, selecting transformants, or amplifying the genesencoding the desired sequences.

Transformation means introducing DNA into the prokaryotic host so thatthe DNA is replicable, either as an extrachromosomal element or bychromosomal integrant. Depending on the host cell used, transformationis done using standard techniques appropriate to such cells. The calciumtreatment employing calcium chloride is generally used for bacterialcells that contain substantial cell-wall barriers. Another method fortransformation employs polyethylene glycol/DMSO. Yet another techniqueused is electroporation.

Prokaryotic cells used to produce the polypeptides of the invention aregrown in media known in the art and suitable for culture of the selectedhost cells. Examples of suitable media include luria broth (LB) plusnecessary nutrient supplements. In some embodiments, the media alsocontains a selection agent, chosen based on the construction of theexpression vector, to selectively permit growth of prokaryotic cellscontaining the expression vector. For example, ampicillin is added tomedia for growth of cells expressing ampicillin resistant gene.

Any necessary supplements besides carbon, nitrogen, and inorganicphosphate sources may also be included at appropriate concentrationsintroduced alone or as a mixture with another supplement or medium suchas a complex nitrogen source. Optionally the culture medium may containone or more reducing agents selected from the group consisting ofglutathione, cysteine, cystamine, thioglycollate, dithioerythritol anddithiothreitol.

The prokaryotic host cells are cultured at suitable temperatures. For E.coli growth, for example, the preferred temperature ranges from about20° C. to about 39° C., more preferably from about 25° C. to about 37°C., even more preferably at about 30° C. The pH of the medium may be anypH ranging from about 5 to about 9, depending mainly on the hostorganism. For E. coli, the pH is preferably from about 6.8 to about 7.4,and more preferably about 7.0.

If an inducible promoter is used in the expression vector of theinvention, protein expression is induced under conditions suitable forthe activation of the promoter. In one aspect of the invention, PhoApromoters are used for controlling transcription of the polypeptides.Accordingly, the transformed host cells are cultured in aphosphate-limiting medium for induction. Preferably, thephosphate-limiting medium is the C.R.A.P medium (see, e.g., Simmons etal., J. Immunol. Methods (2002), 263:133-147). A variety of otherinducers may be used, according to the vector construct employed, as isknown in the art.

In one embodiment, the expressed polypeptides of the present inventionare secreted into and recovered from the periplasm of the host cells.Protein recovery typically involves disrupting the microorganism,generally by such means as osmotic shock, sonication or lysis. Oncecells are disrupted, cell debris or whole cells may be removed bycentrifugation or filtration. The proteins may be further purified, forexample, by affinity resin chromatography. Alternatively, proteins canbe transported into the culture media and isolated therein. Cells may beremoved from the culture and the culture supernatant being filtered andconcentrated for further purification of the proteins produced. Theexpressed polypeptides can be further isolated and identified usingcommonly known methods such as polyacrylamide gel electrophoresis (PAGE)and Western blot assay.

In one aspect of the invention, antibody production is conducted inlarge quantity by a fermentation process. Various large-scale fed-batchfermentation procedures are available for production of recombinantproteins. Large-scale fermentations have at least 1000 liters ofcapacity, preferably about 1,000 to 100,000 liters of capacity. Thesefermentors use agitator impellers to distribute oxygen and nutrients,especially glucose (the preferred carbon/energy source). Small scalefermentation refers generally to fermentation in a fermentor that is nomore than approximately 100 liters in volumetric capacity, and can rangefrom about 1 liter to about 100 liters.

In a fermentation process, induction of protein expression is typicallyinitiated after the cells have been grown under suitable conditions to adesired density, e.g., an OD550 of about 180-220, at which stage thecells are in the early stationary phase. A variety of inducers may beused, according to the vector construct employed, as is known in the artand described above. Cells may be grown for shorter periods prior toinduction. Cells are usually induced for about 12-50 hours, althoughlonger or shorter induction time may be used.

To improve the production yield and quality of the polypeptides of theinvention, various fermentation conditions can be modified. For example,to improve the proper assembly and folding of the secreted antibodypolypeptides, additional vectors overexpressing chaperone proteins, suchas Dsb proteins (DsbA, DsbB, DsbC, DsbD and or DsbG) or FkpA (apeptidylprolyl cis,trans-isomerase with chaperone activity) can be usedto co-transform the host prokaryotic cells. The chaperone proteins havebeen demonstrated to facilitate the proper folding and solubility ofheterologous proteins produced in bacterial host cells. Chen et al.(1999) J Bio Chem 274:19601-19605; Georgiou et al., U.S. Pat. No.6,083,715; Georgiou et al., U.S. Pat. No. 6,027,888; Bothmann andPluckthun (2000) J. Biol. Chem. 275:17100-17105; Ramm and Pluckthun(2000) J. Biol. Chem. 275:17106-17113; Arie et al. (2001) Mol.Microbiol. 39:199-210.

To minimize proteolysis of expressed heterologous proteins (especiallythose that are proteolytically sensitive), certain host strainsdeficient for proteolytic enzymes can be used for the present invention.For example, host cell strains may be modified to effect geneticmutation(s) in the genes encoding known bacterial proteases such asProtease III, OmpT, DegP, Tsp, Protease I, Protease Mi, Protease V,Protease VI and combinations thereof. Some E. coli protease-deficientstrains are available and described in, for example, Joly et al. (1998),supra; Georgiou et al., U.S. Pat. No. 5,264,365; Georgiou et al., U.S.Pat. No. 5,508,192; Hara et al., Microbial Drug Resistance, 2:63-72(1996).

In one embodiment, E. coli strains deficient for proteolytic enzymes andtransformed with plasmids overexpressing one or more chaperone proteinsare used as host cells in the expression system of the invention.

iii. Antibody Purification

Standard protein purification methods known in the art can be employed.The following procedures are exemplary of suitable purificationprocedures: fractionation on immunoaffinity or ion-exchange columns,ethanol precipitation, reverse phase HPLC, chromatography on silica oron a cation-exchange resin such as DEAE, chromatofocusing, SDS-PAGE,ammonium sulfate precipitation, and gel filtration using, for example,Sephadex G-75.

In one aspect, Protein A immobilized on a solid phase is used forimmunoaffinity purification of the full length antibody products of theinvention. Protein A is a 41kD cell wall protein from Staphylococcusaureas which binds with a high affinity to the Fc region of antibodies.Lindmark et al (1983) J. Immunol. Meth. 62:1-13. The solid phase towhich Protein A is immobilized is preferably a column comprising a glassor silica surface, more preferably a controlled pore glass column or asilicic acid column. In some applications, the column has been coatedwith a reagent, such as glycerol, in an attempt to prevent nonspecificadherence of contaminants.

As the first step of purification, the preparation derived from the cellculture as described above is applied onto the Protein A immobilizedsolid phase to allow specific binding of the antibody of interest toProtein A. The solid phase is then washed to remove contaminantsnon-specifically bound to the solid phase. Finally the antibody ofinterest is recovered from the solid phase by elution.

b. Generating Antibodies using Eukaryotic Host Cells:

The vector components generally include, but are not limited to, one ormore of the following: a signal sequence, an origin of replication, oneor more marker genes, an enhancer element, a promoter, and atranscription termination sequence.

(i) Signal Sequence Component

A vector for use in a eukaryotic host cell may also contain a signalsequence or other polypeptide having a specific cleavage site at theN-terminus of the mature protein or polypeptide of interest. Theheterologous signal sequence selected preferably is one that isrecognized and processed (i.e., cleaved by a signal peptidase) by thehost cell. In mammalian cell expression, mammalian signal sequences aswell as viral secretory leaders, for example, the herpes simplex gDsignal, are available.

The DNA for such precursor region is ligated in reading frame to DNAencoding the antibody.

(ii) Origin of Replication

Generally, an origin of replication component is not needed formammalian expression vectors. For example, the SV40 origin may typicallybe used only because it contains the early promoter.

(iii) Selection Gene Component

Expression and cloning vectors may contain a selection gene, also termeda selectable marker. Typical selection genes encode proteins that (a)confer resistance to antibiotics or other toxins, e.g., ampicillin,neomycin, methotrexate, or tetracycline, (b) complement auxotrophicdeficiencies, where relevant, or (c) supply critical nutrients notavailable from complex media.

One example of a selection scheme utilizes a drug to arrest growth of ahost cell. Those cells that are successfully transformed with aheterologous gene produce a protein conferring drug resistance and thussurvive the selection regimen. Examples of such dominant selection usethe drugs neomycin, mycophenolic acid and hygromycin.

Another example of suitable selectable markers for mammalian cells arethose that enable the identification of cells competent to take up theantibody nucleic acid, such as DHFR, thymidine kinase, metallothionein-Iand -II, preferably primate metallothionein genes, adenosine deaminase,ornithine decarboxylase, etc.

For example, cells transformed with the DHFR selection gene are firstidentified by culturing all of the transformants in a culture mediumthat contains methotrexate (Mtx), a competitive antagonist of DHFR. Anappropriate host cell when wild-type DHFR is employed is the Chinesehamster ovary (CHO) cell line deficient in DHFR activity (e.g., ATCCCRL-9096).

Alternatively, host cells (particularly wild-type hosts that containendogenous DHFR) transformed or co-transformed with DNA sequencesencoding an antibody, wild-type DHFR protein, and another selectablemarker such as aminoglycoside 3′-phosphotransferase (APH) can beselected by cell growth in medium containing a selection agent for theselectable marker such as an aminoglycosidic antibiotic, e.g.,kanamycin, neomycin, or G418. See U.S. Pat. No. 4,965,199.

(iv) Promoter Component

Expression and cloning vectors usually contain a promoter that isrecognized by the host organism and is operably linked to the antibodypolypeptide nucleic acid. Promoter sequences are known for eukaryotes.Virtually all eukaryotic genes have an AT-rich region locatedapproximately 25 to 30 bases upstream from the site where transcriptionis initiated. Another sequence found 70 to 80 bases upstream from thestart of transcription of many genes is a CNCAAT region where N may beany nucleotide. At the 3′ end of most eukaryotic genes is an AATAAAsequence that may be the signal for addition of the poly A tail to the3′ end of the coding sequence. All of these sequences are suitablyinserted into eukaryotic expression vectors.

Antibody polypeptide transcription from vectors in mammalian host cellsis controlled, for example, by promoters obtained from the genomes ofviruses such as polyoma virus, fowlpox virus, adenovirus (such asAdenovirus 2), bovine papilloma virus, avian sarcoma virus,cytomegalovirus, a retrovirus, hepatitis-B virus and Simian Virus 40(SV40), from heterologous mammalian promoters, e.g., the actin promoteror an immunoglobulin promoter, from heat-shock promoters, provided suchpromoters are compatible with the host cell systems.

The early and late promoters of the SV40 virus are conveniently obtainedas an SV40 restriction fragment that also contains the SV40 viral originof replication. The immediate early promoter of the humancytomegalovirus is conveniently obtained as a HindIII E restrictionfragment. A system for expressing DNA in mammalian hosts using thebovine papilloma virus as a vector is disclosed in U.S. Pat. No.4,419,446. A modification of this system is described in U.S. Pat. No.4,601,978. Alternatively, the Rous Sarcoma Virus long terminal repeatcan be used as the promoter.

(v) Enhancer Element Component

Transcription of DNA encoding the antibody polypeptide of this inventionby higher eukaryotes is often increased by inserting an enhancersequence into the vector. Many enhancer sequences are now known frommammalian genes (globin, elastase, albumin, α-fetoprotein, and insulin).Typically, however, one will use an enhancer from a eukaryotic cellvirus. Examples include the SV40 enhancer on the late side of thereplication origin (bp 100-270), the cytomegalovirus early promoterenhancer, the polyoma enhancer on the late side of the replicationorigin, and adenovirus enhancers. See also Yaniv, Nature 297:17-18(1982) on enhancing elements for activation of eukaryotic promoters. Theenhancer may be spliced into the vector at a position 5′ or 3′ to theantibody polypeptide-encoding sequence, but is preferably located at asite 5′ from the promoter.

(vi) Transcription Termination Component

Expression vectors used in eukaryotic host cells will typically alsocontain sequences necessary for the termination of transcription and forstabilizing the mRNA. Such sequences are commonly available from the 5′and, occasionally 3′, untranslated regions of eukaryotic or viral DNAsor cDNAs. These regions contain nucleotide segments transcribed aspolyadenylated fragments in the untranslated portion of the mRNAencoding an antibody. One useful transcription termination component isthe bovine growth hormone polyadenylation region. See WO94/11026 and theexpression vector disclosed therein.

(vii) Selection and Transformation of Host Cells

Suitable host cells for cloning or expressing the DNA in the vectorsherein include higher eukaryote cells described herein, includingvertebrate host cells. Propagation of vertebrate cells in culture(tissue culture) has become a routine procedure. Examples of usefulmammalian host cell lines are monkey kidney CV1 line transformed by SV40(COS-7, ATCC CRL 1651); human embryonic kidney line (293 or 293 cellssubcloned for growth in suspension culture, Graham et al., J. Gen Virol.36:59 (1977)); baby hamster kidney cells (BHK, ATCC CCL 10); Chinesehamster ovary cells/−DHFR (CHO, Urlaub et al., Proc. Natl. Acad. Sci.USA 77:4216 (1980)); mouse sertoli cells (TM4, Mather, Biol. Reprod.23:243-251 (1980)); monkey kidney cells (CV1 ATCC CCL 70); African greenmonkey kidney cells (VERO-76, ATCC CRL-1587); human cervical carcinomacells (HELA, ATCC CCL 2); canine kidney cells (MDCK, ATCC CCL 34);buffalo rat liver cells (BRL 3A, ATCC CRL 1442); human lung cells (W138,ATCC CCL 75); human liver cells (Hep G2, HB 8065); mouse mammary tumor(MMT 060562, ATCC CCL51); TR1 cells (Mather et al., Annals N.Y. Acad.Sci. 383:44-68 (1982)); MRC 5 cells; FS4 cells; and a human hepatomaline (Hep G2).

Host cells are transformed with the above-described expression orcloning vectors for antibody production and cultured in conventionalnutrient media modified as appropriate for inducing promoters, selectingtransformants, or amplifying the genes encoding the desired sequences.

(viii) Culturing the Host Cells

The host cells used to produce an antibody of this invention may becultured in a variety of media. Commercially available media such asHam's F 10 (Sigma), Minimal Essential Medium ((MEM), (Sigma), RPMI-1640(Sigma), and Dulbecco's Modified Eagle's Medium ((DMEM), Sigma) aresuitable for culturing the host cells. In addition, any of the mediadescribed in Ham et al., Meth. Enz. 58:44 (1979), Barnes et al., Anal.Biochem. 102:255 (1980), U.S. Pat. No. 4,767,704; 4,657,866; 4,927,762;4,560,655; or 5,122,469; WO 90/03430; WO 87/00195; or U.S. Patent Re.30,985 may be used as culture media for the host cells. Any of thesemedia may be supplemented as necessary with hormones and/or other growthfactors (such as insulin, transferrin, or epidermal growth factor),salts (such as sodium chloride, calcium, magnesium, and phosphate),buffers (such as HEPES), nucleotides (such as adenosine and thymidine),antibiotics (such as GENTAMYCIN™ drug), trace elements (defined asinorganic compounds usually present at final concentrations in themicromolar range), and glucose or an equivalent energy source. Any othernecessary supplements may also be included at appropriate concentrationsthat would be known to those skilled in the art. The culture conditions,such as temperature, pH, and the like, are those previously used withthe host cell selected for expression, and will be apparent to theordinarily skilled artisan.

(ix) Purification of Antibody

When using recombinant techniques, the antibody can be producedintracellularly, or directly secreted into the medium. If the antibodyis produced intracellularly, as a first step, the particulate debris,either host cells or lysed fragments, are removed, for example, bycentrifugation or ultrafiltration. Where the antibody is secreted intothe medium, supernatants from such expression systems are generallyfirst concentrated using a commercially available protein concentrationfilter, for example, an Amicon or Millipore Pellicon ultrafiltrationunit. A protease inhibitor such as PMSF may be included in any of theforegoing steps to inhibit proteolysis and antibiotics may be includedto prevent the growth of adventitious contaminants.

The antibody composition prepared from the cells can be purified using,for example, hydroxylapatite chromatography, gel electrophoresis,dialysis, and affinity chromatography, with affinity chromatographybeing the preferred purification technique. The suitability of protein Aas an affinity ligand depends on the species and isotype of anyimmunoglobulin Fc domain that is present in the antibody. Protein A canbe used to purify antibodies that are based on human λ1, λ2, or λ4 heavychains (Lindmark et al., J. Immunol. Meth. 62:1-13 (1983)). Protein G isrecommended for all mouse isotypes and for human λ3 (Guss et al., EMBOJ. 5:15671575 (1986)). The matrix to which the affinity ligand isattached is most often agarose, but other matrices are available.Mechanically stable matrices such as controlled pore glass orpoly(styrenedivinyl)benzene allow for faster flow rates and shorterprocessing times than can be achieved with agarose. Where the antibodycomprises a CH3 domain, the Bakerbond ABX™resin (J. T. Baker,Phillipsburg, N.J.) is useful for purification. Other techniques forprotein purification such as fractionation on an ion-exchange column,ethanol precipitation, Reverse Phase HPLC, chromatography on silica,chromatography on heparin SEPHAROSE™ chromatography on an anion orcation exchange resin (such as a polyaspartic acid column),chromatofocusing, SDS-PAGE, and ammonium sulfate precipitation are alsoavailable depending on the antibody to be recovered.

Following any preliminary purification step(s), the mixture comprisingthe antibody of interest and contaminants may be subjected to low pHhydrophobic interaction chromatography using an elution buffer at a pHbetween about 2.5-4.5, preferably performed at low salt concentrations(e.g., from about 0-0.25M salt).

Immunoconjugates

The invention also provides immunoconjugates (interchangeably termed“antibody-drug conjugates” or “ADC”), comprising any of the anti-EphB2antibodies described herein conjugated to a cytotoxic agent such as achemotherapeutic agent, a drug, a growth inhibitory agent, a toxin(e.g., an enzymatically active toxin of bacterial, fungal, plant, oranimal origin, or fragments thereof), or a radioactive isotope (i.e., aradioconjugate).

The use of antibody-drug conjugates for the local delivery of cytotoxicor cytostatic agents, i.e. drugs to kill or inhibit tumor cells in thetreatment of cancer (Syrigos and Epenetos (1999) Anticancer Research19:605-614; Niculescu-Duvaz and Springer (1997) Adv. Drg Del. Rev.26:151-172; U.S. Pat. No. 4,975,278) allows targeted delivery of thedrug moiety to tumors, and intracellular accumulation therein, wheresystemic administration of these unconjugated drug agents may result inunacceptable levels of toxicity to normal cells as well as the tumorcells sought to be eliminated (Baldwin et al., (1986) Lancet pp. (Mar.15, 1986):603-05; Thorpe, (1985) “Antibody Carriers Of Cytotoxic AgentsIn Cancer Therapy: A Review,” in Monoclonal Antibodies '84: BiologicalAnd Clinical Applications, A. Pinchera et al. (ed.s), pp. 475-506).Maximal efficacy with minimal toxicity is sought thereby. Bothpolyclonal antibodies and monoclonal antibodies have been reported asuseful in these strategies (Rowland et al., (1986) Cancer Immunol.Immunother., 21:183-87). Drugs used in these methods include daunomycin,doxorubicin, methotrexate, and vindesine (Rowland et al., (1986) supra).Toxins used in antibody-toxin conjugates include bacterial toxins suchas diphtheria toxin, plant toxins such as ricin, small molecule toxinssuch as geldanamycin (Mandler et al (2000) Jour. of the Nat. CancerInst. 92(19):1573-1581; Mandler et al (2000) Bioorganic & Med. Chem.Letters 10:1025-1028; Mandler et al (2002) Bioconjugate Chem.13:786-791), maytansinoids (EP 1391213; Liu et al., (1996) Proc. Natl.Acad. Sci. USA 93:8618-8623), and calicheamicin (Lode et al (1998)Cancer Res. 58:2928; Hinman et al (1993) Cancer Res. 53:3336-3342). Thetoxins may effect their cytotoxic and cytostatic effects by mechanismsincluding tubulin binding, DNA binding, or topoisomerase inhibition.Some cytotoxic drugs tend to be inactive or less active when conjugatedto large antibodies or protein receptor ligands.

ZEVALIN® (ibritumomab tiuxetan, Biogen/Idec) is an antibody-radioisotopeconjugate composed of a murine IgG1 kappa monoclonal antibody directedagainst the CD20 antigen found on the surface of normal and malignant Blymphocytes and ¹¹¹In or ⁹⁰Y radioisotope bound by a thiourealinker-chelator (Wiseman et al (2000) Eur. Jour. Nucl. Med.27(7):766-77; Wiseman et al (2002) Blood 99(12):4336-42; Witzig et al(2002) J. Clin. Oncol. 20(10):2453-63; Witzig et al (2002) J. Clin.Oncol. 20(15):3262-69). Although ZEVALIN has activity against B-cellnon-Hodgkin's Lymphoma (NHL), administration results in severe andprolonged cytopenias in most patients. MYLOTARG™ (gemtuzumab ozogamicin,Wyeth Pharmaceuticals), an antibody drug conjugate composed of a hu CD33antibody linked to calicheamicin, was approved in 2000 for the treatmentof acute myeloid leukemia by injection (Drugs of the Future (2000)25(7):686; U.S. Pat. Nos. 4,970,198; 5,079,233; 5,585,089; 5,606,040;5,693,762; 5,739,116; 5,767,285; 5,773,001). Cantuzumab mertansine(Immunogen, Inc.), an antibody drug conjugate composed of the huC242antibody linked via the disulfide linker SPP to the maytansinoid drugmoiety, DM1, is advancing into Phase II trials for the treatment ofcancers that express CanAg, such as colon, pancreatic, gastric, andothers. MLN-2704 (Millennium Pharm., BZL Biologics, Immunogen Inc.), anantibody drug conjugate composed of the anti-prostate specific membraneantigen (PSMA) monoclonal antibody linked to the maytansinoid drugmoiety, DM1, is under development for the potential treatment ofprostate tumors. The auristatin peptides, auristatin E (AE) andmonomethylauristatin (MMAE), synthetic analogs of dolastatin, wereconjugated to chimeric monoclonal antibodies cBR96 (specific to Lewis Yon carcinomas) and cAC10 (specific to CD30 on hematologicalmalignancies) (Doronina et al (2003) Nature Biotechnology 21(7):778-784)and are under therapeutic development.

Chemotherapeutic agents useful in the generation of immunoconjugates aredescribed herein (above). Enzymatically active toxins and fragmentsthereof that can be used include diphtheria A chain, nonbinding activefragments of diphtheria toxin, exotoxin A chain (from Pseudomonasaeruginosa), ricin A chain, abrin A chain, modeccin A chain,alpha-sarcin, Aleurites fordii proteins, dianthin proteins, Phytolacaamericana proteins (PAPI, PAPII, and PAP-S), momordica charantiainhibitor, curcin, crotin, sapaonaria officinalis inhibitor, gelonin,mitogellin, restrictocin, phenomycin, enomycin, and the tricothecenes.See, e.g., WO 93/21232 published Oct. 28, 1993. A variety ofradionuclides are available for the production of radioconjugatedantibodies. Examples include ²¹²Bi, ¹³¹I, ¹³¹In, ⁹⁰Y, and ¹⁸⁶Re.Conjugates of the antibody and cytotoxic agent are made using a varietyof bifunctional protein-coupling agents such asN-succinimidyl-3-(2-pyridyldithiol) propionate (SPDP), iminothiolane(IT), bifunctional derivatives of imidoesters (such as dimethyladipimidate HCl), active esters (such as disuccinimidyl suberate),aldehydes (such as glutaraldehyde), bis-azido compounds (such as bis(p-azidobenzoyl) hexanediamine), bis-diazonium derivatives (such asbis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such astoluene 2,6-diisocyanate), and bis-active fluorine compounds (such as1,5-difluoro-2,4-dinitrobenzene). For example, a ricin immunotoxin canbe prepared as described in Vitetta et al., Science, 238: 1098 (1987).Carbon-14-labeled 1-isothiocyanatobenzyl-3-methyldiethylenetriaminepentaacetic acid (MX-DTPA) is an exemplary chelating agent forconjugation of radionucleotide to the antibody. See WO94/11026.

Conjugates of an antibody and one or more small molecule toxins, such asa calicheamicin, maytansinoids, dolastatins, aurostatins, atrichothecene, and CC1065, and the derivatives of these toxins that havetoxin activity, are also contemplated herein.

i. Maytansine and Maytansinoids

In some embodiments, the immunoconjugate comprises an antibody (fulllength or fragments) of the invention conjugated to one or moremaytansinoid molecules.

Maytansinoids are mitototic inhibitors which act by inhibiting tubulinpolymerization. Maytansine was first isolated from the east Africanshrub Maytenus serrata (U.S. Pat. No. 3,896,111). Subsequently, it wasdiscovered that certain microbes also produce maytansinoids, such asmaytansinol and C-3 maytansinol esters (U.S. Pat. No. 4,151,042).Synthetic maytansinol and derivatives and analogues thereof aredisclosed, for example, in U.S. Pat. Nos. 4,137,230; 4,248,870;4,256,746; 4,260,608; 4,265,814; 4,294,757; 4,307,016; 4,308,268;4,308,269; 4,309,428; 4,313,946; 4,315,929; 4,317,821; 4,322,348;4,331,598; 4,361,650; 4,364,866; 4,424,219; 4,450,254; 4,362,663; and4,371,533.

Maytansinoid drug moieties are attractive drug moieties in antibody drugconjugates because they are: (i) relatively accessible to prepare byfermentation or chemical modification, derivatization of fermentationproducts, (ii) amenable to derivatization with functional groupssuitable for conjugation through the non-disulfide linkers toantibodies, (iii) stable in plasma, and (iv) effective against a varietyof tumor cell lines.

Exemplary embodiments of maytansinoid drug moieties include: DM1; DM3;and DM4, having the structures:

wherein the wavy line indicates the covalent attachment of the sulfuratom of the drug to a linker (L) of an antibody drug conjugate.

Other exemplary maytansinoid antibody drug conjugates have the followingstructures and abbreviations, (wherein Ab is antibody and p is 1 toabout 8):

Exemplary antibody drug conjugates where DM1 is linked through a BMPEOlinker to a thiol group of the antibody have the structure andabbreviation:

wherein Ab is antibody; n is 0, 1, or 2; and p is 1, 2, 3, or 4.

Immunoconjugates containing maytansinoids, methods of making same, andtheir therapeutic use are disclosed, for example, in U.S. Pat. Nos.5,208,020, 5,416,064 and European Patent EP 0 425 235 B1, thedisclosures of which are hereby expressly incorporated by reference. Liuet al., Proc. Natl. Acad. Sci. USA 93:8618-8623 (1996) describedimmunoconjugates comprising a maytansinoid designated DM1 linked to themonoclonal antibody C242 directed against human colorectal cancer. Theconjugate was found to be highly cytotoxic towards cultured colon cancercells, and showed antitumor activity in an in vivo tumor growth assay.Chari et al., Cancer Research 52:127-131 (1992) describeimmunoconjugates in which a maytansinoid was conjugated via a disulfidelinker to the murine antibody A7 binding to an antigen on human coloncancer cell lines, or to another murine monoclonal antibody TA.1 thatbinds the HER-2/neu oncogene. The cytotoxicity of the TA.1-maytansinoidconjugate was tested in vitro on the human breast cancer cell lineSK-BR-3, which expresses 3×10⁵ HER-2 surface antigens per cell. The drugconjugate achieved a degree of cytotoxicity similar to the freemaytansinoid drug, which could be increased by increasing the number ofmaytansinoid molecules per antibody molecule. The A7-maytansinoidconjugate showed low systemic cytotoxicity in mice.

Antibody-maytansinoid conjugates are prepared by chemically linking anantibody to a maytansinoid molecule without significantly diminishingthe biological activity of either the antibody or the maytansinoidmolecule. See, e.g., U.S. Pat. No. 5,208,020 (the disclosure of which ishereby expressly incorporated by reference). An average of 3-4maytansinoid molecules conjugated per antibody molecule has shownefficacy in enhancing cytotoxicity of target cells without negativelyaffecting the function or solubility of the antibody, although even onemolecule of toxin/antibody would be expected to enhance cytotoxicityover the use of naked antibody. Maytansinoids are well known in the artand can be synthesized by known techniques or isolated from naturalsources. Suitable maytansinoids are disclosed, for example, in U.S. Pat.No. 5,208,020 and in the other patents and nonpatent publicationsreferred to hereinabove. Preferred maytansinoids are maytansinol andmaytansinol analogues modified in the aromatic ring or at otherpositions of the maytansinol molecule, such as various maytansinolesters.

There are many linking groups known in the art for makingantibody-maytansinoid conjugates, including, for example, thosedisclosed in U.S. Pat. No. 5,208,020 or EP Patent 0 425 235 BI, Chari etal., Cancer Research 52:127-131 (1992), and U.S. patent application Ser.No. 10/960,602, filed Oct. 8, 2004, the disclosures of which are herebyexpressly incorporated by reference. Antibody-maytansinoid conjugatescomprising the linker component SMCC may be prepared as disclosed inU.S. patent application Ser. No. 10/960,602, filed Oct. 8, 2004. Thelinking groups include disulfide groups, thioether groups, acid labilegroups, photolabile groups, peptidase labile groups, or esterase labilegroups, as disclosed in the above-identified patents, disulfide andthioether groups being preferred. Additional linking groups aredescribed and exemplified herein.

Conjugates of the antibody and maytansinoid may be made using a varietyof bifunctional protein coupling agents such asN-succinimidyl-3-(2-pyridyldithio) propionate (SPDP),succinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC),iminothiolane (IT), bifunctional derivatives of imidoesters (such asdimethyl adipimidate HCl), active esters (such as disuccinimidylsuberate), aldehydes (such as glutaraldehyde), bis-azido compounds (suchas bis (p-azidobenzoyl) hexanediamine), bis-diazonium derivatives (suchas bis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such astoluene 2,6-diisocyanate), and bis-active fluorine compounds (such as1,5-difluoro-2,4-dinitrobenzene). Particularly preferred coupling agentsinclude N-succinimidyl-3-(2-pyridyldithio) propionate (SPDP) (Carlssonet al., Biochem. J. 173:723-737 (1978)) andN-succinimidyl-4-(2-pyridylthio)pentanoate (SPP) to provide for adisulfide linkage.

The linker may be attached to the maytansinoid molecule at variouspositions, depending on the type of the link. For example, an esterlinkage may be formed by reaction with a hydroxyl group usingconventional coupling techniques. The reaction may occur at the C-3position having a hydroxyl group, the C-14 position modified withhydroxymethyl, the C-15 position modified with a hydroxyl group, and theC-20 position having a hydroxyl group. In a preferred embodiment, thelinkage is formed at the C-3 position of maytansinol or a maytansinolanalogue.

ii. Auristatins and Dolastatins

In some embodiments, the immunoconjugate comprises an antibody of theinvention conjugated to dolastatins or dolostatin peptidic analogs andderivatives, the auristatins (U.S. Pat. Nos. 5,635,483; 5,780,588).Dolastatins and auristatins have been shown to interfere withmicrotubule dynamics, GTP hydrolysis, and nuclear and cellular division(Woyke et al (2001) Antimicrob. Agents and Chemother. 45(12):3580-3584)and have anticancer (U.S. Pat. No. 5,663,149) and antifungal activity(Pettit et al (1998) Antimicrob. Agents Chemother. 42:2961-2965). Thedolastatin or auristatin drug moiety may be attached to the antibodythrough the N (amino) terminus or the C (carboxyl) terminus of thepeptidic drug moiety (WO 02/088172).

Exemplary auristatin embodiments include the N-terminus linkedmonomethylauristatin drug moieties DE and DF, disclosed in“Monomethylvaline Compounds Capable of Conjugation to Ligands”, U.S.Ser. No. 10/983,340, filed Nov. 5, 2004, the disclosure of which isexpressly incorporated by reference in its entirety.

An exemplary auristatin embodiment is MMAE (wherein the wavy lineindicates the covalent attachment to a linker (L) of an antibody drugconjugate).

Another exemplary auristatin embodiment is MMAF (wherein the wavy lineindicates the covalent attachment to a linker (L) of an antibody drugconjugate):

Additional exemplary embodiments comprising MMAE or MMAF and variouslinker components (described further herein) have the followingstructures and abbreviations (wherein Ab means antibody and p is 1 toabout 8):

Typically, peptide-based drug moieties can be prepared by forming apeptide bond between two or more amino acids and/or peptide fragments.Such peptide bonds can be prepared, for example, according to the liquidphase synthesis method (see E. Schröder and K. Lübke, “The Peptides”,volume 1, pp 76-136, 1965, Academic Press) that is well known in thefield of peptide chemistry. The auristatin/dolastatin drug moieties maybe prepared according to the methods of: U.S. Pat. No. 5,635,483; U.S.Pat. No. 5,780,588; Pettit et al (1989) J. Am. Chem. Soc. 111:5463-5465;Pettit et al (1998) Anti-Cancer Drug Design 13:243-277; Pettit, G. R.,et al. Synthesis, 1996, 719-725; and Pettit et al (1996) J. Chem. Soc.Perkin Trans. 1 5:859-863. See also Doronina (2003) Nat Biotechnol21(7):778-784; “Monomethylvaline Compounds Capable of Conjugation toLigands”, U.S. Ser. No. 10/983,340, filed Nov. 5, 2004, herebyincorporated by reference in its entirety (disclosing, e.g., linkers andmethods of preparing monomethylvaline compounds such as MMAE and MMAFconjugated to linkers).

iii. Calicheamicin

In other embodiments, the immunoconjugate comprises an antibody of theinvention conjugated to one or more calicheamicin molecules. Thecalicheamicin family of antibiotics are capable of producingdouble-stranded DNA breaks at sub-picomolar concentrations. For thepreparation of conjugates of the calicheamicin family, see U.S. Pat.Nos. 5,712,374, 5,714,586, 5,739,116, 5,767,285, 5,770,701, 5,770,710,5,773,001, 5,877,296 (all to American Cyanamid Company). Structuralanalogues of calicheamicin which may be used include, but are notlimited to, λ₁ ¹, α₂ ¹, α₃ ¹, N-acetyl-γ₁ ¹, PSAG and θ₁ ¹ (Hinman etal., Cancer Research 53:3336-3342 (1993), Lode et al., Cancer Research58:2925-2928 (1998) and the aforementioned U.S. patents to AmericanCyanamid). Another anti-tumor drug that the antibody can be conjugatedis QFA which is an antifolate. Both calicheamicin and QFA haveintracellular sites of action and do not readily cross the plasmamembrane. Therefore, cellular uptake of these agents through antibodymediated internalization greatly enhances their cytotoxic effects.

iv. Other Cytotoxic Agents

Other antitumor agents that can be conjugated to the antibodies of theinvention include BCNU, streptozoicin, vincristine and 5-fluorouracil,the family of agents known collectively LL-E33288 complex described inU.S. Pat. Nos. 5,053,394, 5,770,710, as well as esperamicins (U.S. Pat.No. 5,877,296).

Enzymatically active toxins and fragments thereof which can be usedinclude diphtheria A chain, nonbinding active fragments of diphtheriatoxin, exotoxin A chain (from Pseudomonas aeruginosa), ricin A chain,abrin A chain, modeccin A chain, alpha-sarcin, Aleurites fordiiproteins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII,and PAP-S), momordica charantia inhibitor, curcin, crotin, sapaonariaofficinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin,enomycin and the tricothecenes. See, for example, WO 93/21232 publishedOct. 28, 1993.

The present invention further contemplates an immunoconjugate formedbetween an antibody and a compound with nucleolytic activity (e.g., aribonuclease or a DNA endonuclease such as a deoxyribonuclease; DNase).

For selective destruction of the tumor, the antibody may comprise ahighly radioactive atom. A variety of radioactive isotopes are availablefor the production of radioconjugated antibodies. Examples includeAt²¹¹, I¹³¹, I¹²⁵, Y⁹⁰, Re¹⁸⁶, Re¹⁸⁸, Sm¹⁵³, Bi²¹², P³², Pb²¹² andradioactive isotopes of Lu. When the conjugate is used for detection, itmay comprise a radioactive atom for scintigraphic studies, for exampletc^(99m) or I¹²³, or a spin label for nuclear magnetic resonance (NMR)imaging (also known as magnetic resonance imaging, mri), such asiodine-123 again, iodine-131, indium-111, fluorine-19, carbon-13,nitrogen-15, oxygen-17, gadolinium, manganese or iron.

The radio- or other labels may be incorporated in the conjugate in knownways. For example, the peptide may be biosynthesized or may besynthesized by chemical amino acid synthesis using suitable amino acidprecursors involving, for example, fluorine-19 in place of hydrogen.Labels such as tc^(99m) or I¹²³, Re¹⁸⁶, Re¹⁸⁸ and In¹¹¹ can be attachedvia a cysteine residue in the peptide. Yttrium-90 can be attached via alysine residue. The IODOGEN method (Fraker et al (1978) Biochem.Biophys. Res. Commun. 80: 49-57 can be used to incorporate iodine-123.“Monoclonal Antibodies in Immunoscintigraphy” (Chatal, CRC Press 1989)describes other methods in detail.

Conjugates of the antibody and cytotoxic agent may be made using avariety of bifunctional protein coupling agents such asN-succinimidyl-3-(2-pyridyldithio) propionate (SPDP),succinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC),iminothiolane (IT), bifunctional derivatives of imidoesters (such asdimethyl adipimidate HCl), active esters (such as disuccinimidylsuberate), aldehydes (such as glutaraldehyde), bis-azido compounds (suchas bis (p-azidobenzoyl) hexanediamine), bis-diazonium derivatives (suchas bis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such astoluene 2,6-diisocyanate), and bis-active fluorine compounds (such as1,5-difluoro-2,4-dinitrobenzene). For example, a ricin immunotoxin canbe prepared as described in Vitetta et al., Science 238:1098 (1987).Carbon-14-labeled 1-isothiocyanatobenzyl-3-methyldiethylenetriaminepentaacetic acid (MX-DTPA) is an exemplary chelating agent forconjugation of radionucleotide to the antibody. See WO94/11026. Thelinker may be a “cleavable linker” facilitating release of the cytotoxicdrug in the cell. For example, an acid-labile linker,peptidase-sensitive linker, photolabile linker, dimethyl linker ordisulfide-containing linker (Chari et al., Cancer Research 52:127-131(1992); U.S. Pat. No. 5,208,020) may be used.

The compounds of the invention expressly contemplate, but are notlimited to, ADC prepared with cross-linker reagents: BMPS, EMCS, GMBS,HBVS, LC-SMCC, MBS, MPBH, SBAP, SIA, SIAB, SMCC, SMPB, SMPH, sulfo-EMCS,sulfo-GMBS, sulfo-KMUS, sulfo-MBS, sulfo-SIAB, sulfo-SMCC, andsulfo-SMPB, and SVSB (succinimidyl-(4-vinylsulfone)benzoate) which arecommercially available (e.g., from Pierce Biotechnology, Inc., Rockford,Ill., U.S.A). See pages 467-498, 2003-2004 Applications Handbook andCatalog.

v. Preparation of Antibody Drug Conjugates

In the antibody drug conjugates (ADC) of the invention, an antibody (Ab)is conjugated to one or more drug moieties (D), e.g. about 1 to about 20drug moieties per antibody, through a linker (L). The ADC of Formula Imay be prepared by several routes, employing organic chemistryreactions, conditions, and reagents known to those skilled in the art,including: (1) reaction of a nucleophilic group of an antibody with abivalent linker reagent, to form Ab-L, via a covalent bond, followed byreaction with a drug moiety D; and (2) reaction of a nucleophilic groupof a drug moiety with a bivalent linker reagent, to form D-L, via acovalent bond, followed by reaction with the nucleophilic group of anantibody. Additional methods for preparing ADC are described herein.

Ab-(L-D)_(p)  I

The linker may be composed of one or more linker components. Exemplarylinker components include 6-maleimidocaproyl (“MC”), maleimidopropanoyl(“MP”), valine-citrulline (“val-cit”), alanine-phenylalanine(“ala-phe”), p-aminobenzyloxycarbonyl (“PAB”), N-Succinimidyl4-(2-pyridylthio) pentanoate (“SPP”), N-Succinimidyl4-(N-maleimidomethyl)cyclohexane-1 carboxylate (“SMCC”), andN-Succinimidyl (4-iodo-acetyl) aminobenzoate (“SIAB”). Additional linkercomponents are known in the art and some are described herein. See also“Monomethylvaline Compounds Capable of Conjugation to Ligands”, U.S.Ser. No. 10/983,340, filed Nov. 5, 2004, the contents of which arehereby incorporated by reference in its entirety.

In some embodiments, the linker may comprise amino acid residues.Exemplary amino acid linker components include a dipeptide, atripeptide, a tetrapeptide or a pentapeptide. Exemplary dipeptidesinclude: valine-citrulline (vc or val-cit), alanine-phenylalanine (af orala-phe). Exemplary tripeptides include: glycine-valine-citrulline(gly-val-cit) and glycine-glycine-glycine (gly-gly-gly). Amino acidresidues which comprise an amino acid linker component include thoseoccurring naturally, as well as minor amino acids and non-naturallyoccurring amino acid analogs, such as citrulline. Amino acid linkercomponents can be designed and optimized in their selectivity forenzymatic cleavage by a particular enzymes, for example, atumor-associated protease, cathepsin B, C and D, or a plasmin protease.

Exemplary linker component structures are shown below (wherein the wavyline indicates sites of covalent attachment to other components of theADC):

Additional exemplary linker components and abbreviations include(wherein the antibody (Ab) and linker are depicted, and p is 1 to about8):

Nucleophilic groups on antibodies include, but are not limited to: (i)N-terminal amine groups, (ii) side chain amine groups, e.g. lysine,(iii) side chain thiol groups, e.g. cysteine, and (iv) sugar hydroxyl oramino groups where the antibody is glycosylated. Amine, thiol, andhydroxyl groups are nucleophilic and capable of reacting to formcovalent bonds with electrophilic groups on linker moieties and linkerreagents including: (i) active esters such as NHS esters, HOBt esters,haloformates, and acid halides; (ii) alkyl and benzyl halides such ashaloacetamides; (iii) aldehydes, ketones, carboxyl, and maleimidegroups. Certain antibodies have reducible interchain disulfides, i.e.cysteine bridges. Antibodies may be made reactive for conjugation withlinker reagents by treatment with a reducing agent such as DTT(dithiothreitol). Each cysteine bridge will thus form, theoretically,two reactive thiol nucleophiles. Additional nucleophilic groups can beintroduced into antibodies through the reaction of lysines with2-iminothiolane (Traut's reagent) resulting in conversion of an amineinto a thiol. Reactive thiol groups may be introduced into the antibody(or fragment thereof) by introducing one, two, three, four, or morecysteine residues (e.g., preparing mutant antibodies comprising one ormore non-native cysteine amino acid residues).

Antibody drug conjugates of the invention may also be produced bymodification of the antibody to introduce electrophilic moieties, whichcan react with nucleophilic substituents on the linker reagent or drug.The sugars of glycosylated antibodies may be oxidized, e.g. withperiodate oxidizing reagents, to form aldehyde or ketone groups whichmay react with the amine group of linker reagents or drug moieties. Theresulting imine Schiff base groups may form a stable linkage, or may bereduced, e.g. by borohydride reagents to form stable amine linkages. Inone embodiment, reaction of the carbohydrate portion of a glycosylatedantibody with either glactose oxidase or sodium meta-periodate may yieldcarbonyl (aldehyde and ketone) groups in the protein that can react withappropriate groups on the drug (Hermanson, Bioconjugate Techniques). Inanother embodiment, proteins containing N-terminal serine or threonineresidues can react with sodium meta-periodate, resulting in productionof an aldehyde in place of the first amino acid (Geoghegan & Stroh,(1992) Bioconjugate Chem. 3:138-146; U.S. Pat. No. 5,362,852). Suchaldehyde can be reacted with a drug moiety or linker nucleophile.

Likewise, nucleophilic groups on a drug moiety include, but are notlimited to: amine, thiol, hydroxyl, hydrazide, oxime, hydrazine,thiosemicarbazone, hydrazine carboxylate, and arylhydrazide groupscapable of reacting to form covalent bonds with electrophilic groups onlinker moieties and linker reagents including: (i) active esters such asNHS esters, HOBt esters, haloformates, and acid halides; (ii) alkyl andbenzyl halides such as haloacetamides; (iii) aldehydes, ketones,carboxyl, and maleimide groups.

Alternatively, a fusion protein comprising the antibody and cytotoxicagent may be made, e.g., by recombinant techniques or peptide synthesis.The length of DNA may comprise respective regions encoding the twoportions of the conjugate either adjacent one another or separated by aregion encoding a linker peptide which does not destroy the desiredproperties of the conjugate.

In yet another embodiment, the antibody may be conjugated to a“receptor” (such streptavidin) for utilization in tumor pre-targetingwherein the antibody-receptor conjugate is administered to the patient,followed by removal of unbound conjugate from the circulation using aclearing agent and then administration of a “ligand” (e.g., avidin)which is conjugated to a cytotoxic agent (e.g., a radionucleotide).

Antibody (Ab)-MC-MMAE may be prepared by conjugation of any of theantibodies provided herein with MC-MMAE as follows. Antibody, dissolvedin 500 mM sodium borate and 500 mM sodium chloride at pH 8.0 is treatedwith an excess of 100 mM dithiothreitol (DTT). After incubation at 37°C. for about 30 minutes, the buffer is exchanged by elution overSephadex G25 resin and eluted with PBS with 1 mM DTPA. The thiol/Abvalue is checked by determining the reduced antibody concentration fromthe absorbance at 280 nm of the solution and the thiol concentration byreaction with DTNB (Aldrich, Milwaukee, Wis.) and determination of theabsorbance at 412 nm. The reduced antibody dissolved in PBS is chilledon ice. The drug linker reagent, maleimidocaproyl-monomethyl auristatinE (MMAE), i.e. MC-MMAE, dissolved in DMSO, is diluted in acetonitrileand water at known concentration, and added to the chilled reducedantibody 2H9 in PBS. After about one hour, an excess of maleimide isadded to quench the reaction and cap any unreacted antibody thiolgroups. The reaction mixture is concentrated by centrifugalultrafiltration and 2H9-MC-MMAE is purified and desalted by elutionthrough G25 resin in PBS, filtered through 0.2 μm filters under sterileconditions, and frozen for storage.

Antibody-MC-MMAF may be prepared by conjugation of any of the antibodiesprovided herein with MC-MMAF following the protocol provided forpreparation of Ab-MC-MMAE.

Antibody-MC-val-cit-PAB-MMAE may be prepared by conjugation of any ofthe antibodies provided herein with MC-val-cit-PAB-MMAE following theprotocol provided for preparation of Ab-MC-MMAE.

Antibody-MC-val-cit-PAB-MMAF may be prepared by conjugation of any ofthe antibodies provided herein with MC-val-cit-PAB-MMAF following theprotocol provided for preparation of Ab-MC-MMAE.

Antibody-SMCC-DM1 may be prepared by conjugation of any of theantibodies provided herein with SMCC-DM1 as follows. Purified antibodyis derivatized with (Succinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC, Pierce Biotechnology, Inc) to introducethe SMCC linker. Specifically, antibody is treated at 20 mg/mL in 50 mMpotassium phosphate/50 mM sodium chloride/2 mM EDTA, pH 6.5 with 7.5molar equivalents of SMCC (20 mM in DMSO, 6.7 mg/mL). After stirring for2 hours under argon at ambient temperature, the reaction mixture isfiltered through a Sephadex G25 column equilibrated with 50 mM potassiumphosphate/50 mM sodium chloride/2 mM EDTA, pH 6.5. Antibody containingfractions are pooled and assayed.

Antibody-SMCC prepared thus is diluted with 50 mM potassium phosphate/50mM sodium chloride/2 mM EDTA, pH 6.5, to a final concentration of about10 mg/ml, and reacted with a 10 mM solution of DM1 in dimethylacetamide.The reaction is stirred at ambient temperature under argon 16.5 hours.The conjugation reaction mixture is filtered through a Sephadex G25 gelfiltration column (1.5×4.9 cm) with 1×PBS at pH 6.5. The DM1 drug toantibody ratio (p) may be about 2 to 5, as measured by the absorbance at252 nm and at 280 nm.

Ab-SPP-DM1 may be prepared by conjugation of any of the antibodiesprovided herein with SPP-DM1 as follows. Purified antibody isderivatized with N-succinimidyl-4-(2-pyridylthio)pentanoate to introducedithiopyridyl groups. Antibody (376.0 mg, 8 mg/mL) in 44.7 mL of 50 mMpotassium phosphate buffer (pH 6.5) containing NaCl (50 mM) and EDTA (1mM) is treated with SPP (5.3 molar equivalents in 2.3 mL ethanol). Afterincubation for 90 minutes under argon at ambient temperature, thereaction mixture is gel filtered through a Sephadex G25 columnequilibrated with 35 mM sodium citrate, 154 mM NaCl, 2 mM EDTA. Antibodycontaining fractions were pooled and assayed. The degree of modificationof the antibody is determined as described above.

Antibody-SPP-Py (about 10 μmoles of releasable 2-thiopyridine groups) isdiluted with the above 35 mM sodium citrate buffer, pH 6.5, to a finalconcentration of about 2.5 mg/mL. DM1 (1.7 equivalents, 17 μmoles) in3.0 mM dimethylacetamide (DMA, 3% v/v in the final reaction mixture) isthen added to the antibody solution. The reaction proceeds at ambienttemperature under argon for about 20 hours. The reaction is loaded on aSephacryl S300 gel filtration column (5.0 cm×90.0 cm, 1.77 L)equilibrated with 35 mM sodium citrate, 154 mM NaCl, pH 6.5. The flowrate may be about 5.0 mL/min and 65 fractions (20.0 mL each) arecollected. The number of DM1 drug molecules linked per antibody molecule(p′) is determined by measuring the absorbance at 252 nm and 280 nm, andmay be about 2 to 4 DM1 drug moieties per antibody.

Antibody-BMPEO-DM1 may be prepared by conjugation of any of theantibodies provided herein with BMPEO-DM1 as follows. The antibody ismodified by the bis-maleimido reagent BM(PEO)₄ (Pierce Chemical),leaving an unreacted maleimido group on the surface of the antibody.This may be accomplished by dissolving BM(PEO)₄ in a 50% ethanol/watermixture to a concentration of 10 mM and adding a tenfold molar excess toa solution containing antibody in phosphate buffered saline at aconcentration of approximately 1.6 mg/ml (10 micromolar) and allowing itto react for 1 hour to form antibody-linker intermediate,antibody-BMPEO. Excess BM(PEO)₄ is removed by gel filtration (HiTrapcolumn, Pharmacia) in 30 mM citrate, pH 6 with 150 mM NaCl buffer. Anapproximate 10 fold molar excess DM1 is dissolved in dimethyl acetamide(DMA) and added to the antibody-BMPEO intermediate. Dimethyl formamide(DMF) may also be employed to dissolve the drug moiety reagent. Thereaction mixture is allowed to react overnight before gel filtration ordialysis into PBS to remove unreacted DM1. Gel filtration on S200columns in PBS is used to remove high molecular weight aggregates andfurnish purified antibody-BMPEO-DM1.

Pharmaceutical Formulations

Therapeutic formulations comprising an antibody of the invention areprepared for storage by mixing the antibody having the desired degree ofpurity with optional physiologically acceptable carriers, excipients orstabilizers (Remington: The Science and Practice of Pharmacy 20thedition (2000)), in the form of aqueous solutions, lyophilized or otherdried formulations. Acceptable carriers, excipients, or stabilizers arenontoxic to recipients at the dosages and concentrations employed, andinclude buffers such as phosphate, citrate, histidine and other organicacids; antioxidants including ascorbic acid and methionine;preservatives (such as octadecyldimethylbenzyl ammonium chloride;hexamethonium chloride; benzalkonium chloride, benzethonium chloride;phenol, butyl or benzyl alcohol; alkyl parabens such as methyl or propylparaben; catechol; resorcinol; cyclohexanol; 3-pentanol; and m-cresol);low molecular weight (less than about 10 residues) polypeptides;proteins, such as serum albumin, gelatin, or immunoglobulins;hydrophilic polymers such as polyvinylpyrrolidone; amino acids such asglycine, glutamine, asparagine, histidine, arginine, or lysine;monosaccharides, disaccharides, and other carbohydrates includingglucose, mannose, or dextrins; chelating agents such as EDTA; sugarssuch as sucrose, mannitol, trehalose or sorbitol; salt-formingcounter-ions such as sodium; metal complexes (e.g., Zn-proteincomplexes); and/or non-ionic surfactants such as TWEEN™, PLURONICS™ orpolyethylene glycol (PEG).

The formulation herein may also contain more than one active compound asnecessary for the particular indication being treated, preferably thosewith complementary activities that do not adversely affect each other.Such molecules are suitably present in combination in amounts that areeffective for the purpose intended.

The active ingredients may also be entrapped in microcapsule prepared,for example, by coacervation techniques or by interfacialpolymerization, for example, hydroxymethylcellulose orgelatin-microcapsule and poly-(methylmethacylate) microcapsule,respectively, in colloidal drug delivery systems (for example,liposomes, albumin microspheres, microemulsions, nano-particles andnanocapsules) or in macroemulsions. Such techniques are disclosed inRemington: The Science and Practice of Pharmacy 20th edition (2000).

The formulations to be used for in vivo administration must be sterile.This is readily accomplished by filtration through sterile filtrationmembranes.

Sustained-release preparations may be prepared. Suitable examples ofsustained-release preparations include semipermeable matrices of solidhydrophobic polymers containing the immunoglobulin of the invention,which matrices are in the form of shaped articles, e.g., films, ormicrocapsule. Examples of sustained-release matrices include polyesters,hydrogels (for example, poly(2-hydroxyethyl-methacrylate), orpoly(vinylalcohol)), polylactides (U.S. Pat. No. 3,773,919), copolymersof L-glutamic acid and γ ethyl-L-glutamate, non-degradableethylene-vinyl acetate, degradable lactic acid-glycolic acid copolymerssuch as the LUPRON DEPOT™ (injectable microspheres composed of lacticacid-glycolic acid copolymer and leuprolide acetate), andpoly-D-(−)-3-hydroxybutyric acid. While polymers such as ethylene-vinylacetate and lactic acid-glycolic acid enable release of molecules forover 100 days, certain hydrogels release proteins for shorter timeperiods. When encapsulated immunoglobulins remain in the body for a longtime, they may denature or aggregate as a result of exposure to moistureat 37° C., resulting in a loss of biological activity and possiblechanges in immunogenicity. Rational strategies can be devised forstabilization depending on the mechanism involved. For example, if theaggregation mechanism is discovered to be intermolecular S—S bondformation through thio-disulfide interchange, stabilization may beachieved by modifying sulfhydryl residues, lyophilizing from acidicsolutions, controlling moisture content, using appropriate additives,and developing specific polymer matrix compositions.

Uses

An antibody of the present invention may be used in, for example, invitro, ex vivo and in vivo therapeutic methods.

In one aspect, the invention provides methods for treating or preventinga tumor, a cancer, and/or a cell proliferative disorder associated withincreased expression and/or activity of EphB2, the methods comprisingadministering an effective amount of an anti-EphB2 antibody orimmunoconjugate to a subject in need of such treatment.

In one aspect, the invention provides methods for killing a tumor cell,the methods comprising administering an effective amount of ananti-EphB2 antibody or immunoconjugate (in some embodiments, ananti-EphB2 antibody or immunoconjugate of the invention) to a subject inneed of such treatment.

In one aspect, the invention provides methods for reducing, inhibiting,or preventing growth of a tumor or cancer, the methods comprisingadministering an effective amount of an anti-EphB2 antibody orimmunoconjugate to a subject in need of such treatment.

Moreover, at least some of the antibodies of the invention can bindantigen from other species. Accordingly, the antibodies of the inventioncan be used to bind specific antigen activity, e.g., in a cell culturecontaining the antigen, in human subjects or in other mammalian subjectshaving the antigen with which an antibody of the invention cross-reacts(e.g. chimpanzee, baboon, marmoset, cynomolgus and rhesus, pig ormouse). In one embodiment, the antibody of the invention can be used forinhibiting antigen activities by contacting the antibody with theantigen such that antigen activity is inhibited. Preferably, the antigenis a human protein molecule.

In one embodiment, an antibody of the invention can be used in a methodfor binding an antigen in a subject suffering from a disorder associatedwith increased antigen expression and/or activity, comprisingadministering to the subject an antibody of the invention such that theantigen in the subject is bound. Preferably, the antigen is a humanprotein molecule and the subject is a human subject. Alternatively, thesubject can be a mammal expressing the antigen with which an antibody ofthe invention binds. Still further the subject can be a mammal intowhich the antigen has been introduced (e.g., by administration of theantigen or by expression of an antigen transgene). An antibody of theinvention can be administered to a human subject for therapeuticpurposes. Moreover, an antibody of the invention can be administered toa non-human mammal expressing an antigen with which the immunoglobulincross-reacts (e.g., a primate, pig or mouse) for veterinary purposes oras an animal model of human disease. Regarding the latter, such animalmodels may be useful for evaluating the therapeutic efficacy ofantibodies of the invention (e.g., testing of dosages and time coursesof administration).

The antibodies of the invention can be used to treat, inhibit, delayprogression of, prevent/delay recurrence of, ameliorate, or preventdiseases, disorders or conditions associated with expression and/oractivity of one or more antigen molecules.

Exemplary disorders include carcinoma, lymphoma, blastoma, sarcoma, andleukemia or lymphoid malignancies. More particular examples of suchcancers include squamous cell cancer (e.g., epithelial squamous cellcancer), lung cancer including small-cell lung cancer, non-small celllung cancer, adenocarcinoma of the lung and squamous carcinoma of thelung, cancer of the peritoneum, hepatocellular cancer, gastric orstomach cancer including gastrointestinal cancer, pancreatic cancer,glioblastoma, cervical cancer, ovarian cancer, liver cancer, bladdercancer, cancer of the urinary tract, hepatoma, breast cancer, coloncancer, rectal cancer, colorectal cancer, endometrial or uterinecarcinoma, salivary gland carcinoma, kidney or renal cancer, prostatecancer, vulval cancer, thyroid cancer, hepatic carcinoma, analcarcinoma, penile carcinoma, melanoma, multiple myeloma and B-celllymphoma, brain, as well as head and neck cancer, and associatedmetastases. In some embodiments, the cancer is selected from the groupconsisting of small cell lung cancer, neuroblastomas, melanoma, breastcarcinoma, gastric cancer, colorectal cancer (CRC), and hepatocellularcarcinoma. In some embodiments, the cancer is colorectal cancer.

The antibodies of the invention are also useful in the treatment(including prevention) of disorders the pathology of which involvescellular degeneration or dysfunction, such as treatment of various(chronic) neurodegenerative disorders and acute nerve cell injuries.Such neurodegenerative disorders include, without limitation, peripheralneuropathies; motorneuron disorders, such as amylotrophic lateralsclerosis (ALS, Lou Gehrig's disease), Bell's palsy, and variousconditions involving spinal muscular atrophy or paralysis; and otherhuman neurodegenerative diseases, such as Alzheimer's disease,Parkinson's disease, epilepsy, multiple sclerosis, Huntington's chorea,Down's Syndrome, nerve deafness, and Meniere's disease, and acute nervecell injuries, for example due to trauma or spinal cord injury.

The antibodies of the invention are also useful for inhibitingangiogenesis. In some embodiments, the site of angiogenesis is a tumoror cancer.

In some embodiments, the disorder is characterized by colon adenoma(s).The methods of the invention are particularly suitable for disorderscharacterized by a plurality of colon adenomas (such as more than 10,20, 30, 40, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, ormore colon adenomas), including at least the following: autosomaldominant familial adenomatous polyposis (FAP) disorder caused bymutation in the APC gene (Tomlinson et al., J Med Genet. 1996;33:268-73); Peutz-Jegher's syndrome (PJS), Juvenile Polyposis Syndrome(JPS), Attenuated FAP caused by mutations in the MYH gene (Sieber et al.N Eng J Med 348:791-9 (2003)), Hereditary Mixed Polyposis syndrome(HMPS), Cowden disease, and Bannayan-Ruvalcaba-Riley syndrome.

EphB2 has been implicated in motoaxon guidance and neural crest cellmigration in the developing embryo. Accordingly, the antibodies of theinvention are also useful for modulating axon guidance, neuronaldevelopment, and/or neural crest migration in vitro or in vivo.

In certain embodiments, an immunoconjugate comprising an antibodyconjugated with one or more cytotoxic agent(s) is administered to thepatient. In some embodiments, the immunoconjugate and/or antigen towhich it is bound is/are internalized by the cell, resulting inincreased therapeutic efficacy of the immunoconjugate in killing thetarget cell to which it binds. In one embodiment, the cytotoxic agenttargets or interferes with nucleic acid in the target cell. In oneembodiment, the cytotoxic agent targets or interferes with microtubulepolymerization. Examples of such cytotoxic agents include any of thechemotherapeutic agents noted herein (such as a maytansinoid,auristatin, dolastatin, or a calicheamicin), a radioactive isotope, or aribonuclease or a DNA endonuclease.

Antibodies and immunoconjugates of the invention can be used eitheralone or in combination with other compositions in a therapy. Forinstance, an antibody of the invention may be co-administered withanother antibody, chemotherapeutic agent(s) (including cocktails ofchemotherapeutic agents), other cytotoxic agent(s), anti-angiogenicagent(s), cytokines, and/or growth inhibitory agent(s). Where anantibody of the invention inhibits tumor growth, it may be particularlydesirable to combine it with one or more other therapeutic agent(s)which also inhibits tumor growth. For instance, anti-VEGF antibodiesblocking VEGF activities may be combined with anti-ErbB antibodies (e.g.HERCEPTIN® anti-HER2 antibody) in a treatment of metastatic breastcancer. Alternatively, or additionally, the patient may receive combinedradiation therapy (e.g. external beam irradiation or therapy with aradioactive labeled agent, such as an antibody). Such combined therapiesnoted above include combined administration (where the two or moreagents are included in the same or separate formulations), and separateadministration, in which case, administration of the antibody of theinvention can occur prior to, and/or following, administration of theadjunct therapy or therapies.

The antibody of the invention (and adjunct therapeutic agent) is/areadministered by any suitable means, including parenteral, subcutaneous,intraperitoneal, intrapulmonary, and intranasal, and, if desired forlocal treatment, intralesional administration. Parenteral infusionsinclude intramuscular, intravenous, intraarterial, intraperitoneal, orsubcutaneous administration. In addition, the antibody is suitablyadministered by pulse infusion, particularly with declining doses of theantibody. Dosing can be by any suitable route, e.g. by injections, suchas intravenous or subcutaneous injections, depending in part on whetherthe administration is brief or chronic.

The antibody composition of the invention will be formulated, dosed, andadministered in a fashion consistent with good medical practice. Factorsfor consideration in this context include the particular disorder beingtreated, the particular mammal being treated, the clinical condition ofthe individual patient, the cause of the disorder, the site of deliveryof the agent, the method of administration, the scheduling ofadministration, and other factors known to medical practitioners. Theantibody need not be, but is optionally formulated with one or moreagents currently used to prevent or treat the disorder in question. Theeffective amount of such other agents depends on the amount ofantibodies of the invention present in the formulation, the type ofdisorder or treatment, and other factors discussed above. These aregenerally used in the same dosages and with administration routes asused hereinbefore or about from 1 to 99% of the heretofore employeddosages.

For the prevention or treatment of disease, the appropriate dosage of anantibody of the invention (when used alone or in combination with otheragents such as chemotherapeutic agents) will depend on the type ofdisease to be treated, the type of antibody, the severity and course ofthe disease, whether the antibody is administered for preventive ortherapeutic purposes, previous therapy, the patient's clinical historyand response to the antibody, and the discretion of the attendingphysician. The antibody is suitably administered to the patient at onetime or over a series of treatments. Depending on the type and severityof the disease, about 1 μg/kg to 15 mg/kg (e.g. 0.1 mg/kg-10 mg/kg) ofantibody is an initial candidate dosage for administration to thepatient, whether, for example, by one or more separate administrations,or by continuous infusion. One typical daily dosage might range fromabout 1 μg/kg to 100 mg/kg or more, depending on the factors mentionedabove. For repeated administrations over several days or longer,depending on the condition, the treatment is sustained until a desiredsuppression of disease symptoms occurs. One exemplary dosage of theantibody would be in the range from about 0.05 mg/kg to about 10 mg/kg.Thus, one or more doses of about 0.5 mg/kg, 2.0 mg/kg, 4.0 mg/kg or 10mg/kg (or any combination thereof) may be administered to the patient.Such doses may be administered intermittently, e.g. every week or everythree weeks (e.g. such that the patient receives from about two to abouttwenty, e.g. about six doses of the antibody). An initial higher loadingdose, followed by one or more lower doses may be administered. Anexemplary dosing regimen comprises administering an initial loading doseof about 4 mg/kg, followed by a weekly maintenance dose of about 2 mg/kgof the antibody. However, other dosage regimens may be useful. Theprogress of this therapy is easily monitored by conventional techniquesand assays.

The anti-EphB2 antibodies of the invention are useful in assaysdetecting EphB2 expression (such as diagnostic or prognostic assays) inspecific cells or tissues wherein the antibodies are labeled asdescribed below and/or are immobilized on an insoluble matrix.

In another aspect, the invention provides methods for detection ofEphB2, the methods comprising detecting EphB2-anti-EphB2 antibodycomplex in the sample. The term “detection” as used herein includesqualitative and/or quantitative detection (measuring levels) with orwithout reference to a control.

In another aspect, the invention provides methods for diagnosing adisorder associated with EphB2 expression and/or activity, the methodscomprising detecting EphB2-anti-EphB2 antibody complex in a biologicalsample from a patient having or suspected of having the disorder. Insome embodiments, the EphB2 expression is increased expression orabnormal (undesired) expression. In some embodiments, the disorder is atumor, cancer, and/or a cell proliferative disorder.

In another aspect, the invention provides methods for evaluation(prognostic evaluation) of a patient having or suspected of havingcancer, the method comprising: (a) obtaining a biological sample fromthe patient; (b) detecting EphB2 expression in the biological sample;(c) comparing EphB2 expression in the biological sample with expressionof EphB2 in a control sample (control reference value); and (d)predicting cancer prognosis of the patient based on the comparison in(a), wherein increased EphB2 expression in the patient biological samplerelative to the control sample is prognostic for cancer in the patient.Increased EphB2 expression is prognostic for cancer. See Jubb et al,U.S. patent application Ser. No. ______, filed Jan. 6, 2005. Thus,determining cancer prognosis can provide for convenient, efficient, andpotentially cost-effective means to obtain data and information usefulin assessing future course of the disorder, including selection ofappropriate therapies for treating patients.

In another aspect, the invention provides any of the anti-EphB2antibodies described herein, wherein the anti-EphB2 antibody comprises adetectable label.

In another aspect, the invention provides a complex of any of theanti-EphB2 antibodies described herein and EphB2. In some embodiments,the complex is in vivo or in vitro. In some embodiments, the complexcomprises a cancer cell. In some embodiments, the anti-EphB2 antibody isdetectably labeled.

Anti-EphB2 antibodies can be used for the detection of EphB2 in any oneof a number of well known detection assay methods. For example, abiological sample may be assayed for EphB2 by obtaining the sample froma desired source, admixing the sample with anti-EphB2 antibody to allowthe antibody to form antibody/EphB2 complex with any EphB2 present inthe mixture, and detecting any antibody/EphB2 complex present in themixture. The biological sample may be prepared for assay by methodsknown in the art which are suitable for the particular sample. Themethods of admixing the sample with antibodies and the methods ofdetecting antibody/EphB2 complex are chosen according to the type ofassay used. Such assays include immunohistochemistry, competitive andsandwich assays, and steric inhibition assays.

Analytical methods for EphB2 all use one or more of the followingreagents: labeled EphB2 analogue, immobilized EphB2 analogue, labeledanti-EphB2 antibody, immobilized anti-EphB2 antibody and stericconjugates. The labeled reagents also are known as “tracers.”

The label used is any detectable functionality that does not interferewith the binding of EphB2 and anti-EphB2 antibody. Numerous labels areknown for use in immunoassay, examples including moieties that may bedetected directly, such as fluorochrome, chemiluminescent, andradioactive labels, as well as moieties, such as enzymes, that must bereacted or derivatized to be detected. Examples of such labels include:The label used is any detectable functionality that does not interferewith the binding of EphB2 and anti-EphB2 antibody. Numerous labels areknown for use in immunoassay, examples including moieties that may bedetected directly, such as fluorochrome, chemiluminescent, andradioactive labels, as well as moieties, such as enzymes, that must bereacted or derivatized to be detected. Examples of such labels includethe radioisotopes ³²P, ¹⁴C, ¹²⁵I, ³H, and ¹³¹I, fluorophores such asrare earth chelates or fluorescein and its derivatives, rhodamine andits derivatives, dansyl, umbelliferone, luceriferases, e.g., fireflyluciferase and bacterial luciferase (U.S. Pat. No. 4,737,456),luciferin, 2,3-dihydrophthalazinediones, horseradish peroxidase (HRP),alkaline phosphatase, β-galactosidase, glucoamylase, lysozyme,saccharide oxidases, e.g., glucose oxidase, galactose oxidase, andglucose-6-phosphate dehydrogenase, heterocyclic oxidases such as uricaseand xanthine oxidase, coupled with an enzyme that employs hydrogenperoxide to oxidize a dye precursor such as HRP, lactoperoxidase, ormicroperoxidase, biotin/avidin, spin labels, bacteriophage labels,stable free radicals, and the like.

Conventional methods are available to bind these labels covalently toproteins or polypeptides. For instance, coupling agents such asdialdehydes, carbodiimides, dimaleimides, bis-imidates, bis-diazotizedbenzidine, and the like may be used to tag the antibodies with theabove-described fluorescent, chemiluminescent, and enzyme labels. See,for example, U.S. Pat. Nos. 3,940,475 (fluorimetry) and 3,645,090(enzymes); Hunter et al., Nature, 144: 945 (1962); David et al.,Biochemistry, 13: 1014-1021 (1974); Pain et al., J. Immuunol. Methods,40: 219-230 (1981); and Nygren, J. Histochem. and Cytochem., 30: 407-412(1982). Preferred labels herein are enzymes such as horseradishperoxidase and alkaline phosphatase. The conjugation of such label,including the enzymes, to the antibody is a standard manipulativeprocedure for one of ordinary skill in immunoassay techniques. See, forexample, O'Sullivan et al., “Methods for the Preparation ofEnzyme-antibody Conjugates for Use in Enzyme Immunoassay,” in Methods inEnzymology, ed. J. J. Langone and H. Van Vunakis, Vol. 73 (AcademicPress, New York, N.Y., 1981), pp. 147-166.

Immobilization of reagents is required for certain assay methods.Immobilization entails separating the anti-EphB2 antibody from any EphB2that remains free in solution. This conventionally is accomplished byeither insolubilizing the anti-EphB2 antibody or EphB2 analogue beforethe assay procedure, as by adsorption to a water-insoluble matrix orsurface (Bennich et al., U.S. Pat. No. 3,720,760), by covalent coupling(for example, using glutaraldehyde cross-linking), or by insolubilizingthe anti-EphB2 antibody or EphB2 analogue afterward, e.g., byimmunoprecipitation.

The expression of proteins in a sample may be examined usingimmunohistochemistry and staining protocols. Immunohistochemicalstaining of tissue sections has been shown to be a reliable method ofassessing or detecting presence of proteins in a sample.Immunohistochemistry (“IHC”) techniques utilize an antibody to probe andvisualize cellular antigens in situ, generally by chromogenic orfluorescent methods. For sample preparation, a tissue or cell samplefrom a mammal (typically a human patient) may be used. Examples ofsamples include, but are not limited to, cancer cells such as colon,breast, prostate, ovary, lung, stomach, pancreas, lymphoma, and leukemiacancer cells. The sample can be obtained by a variety of proceduresknown in the art including, but not limited to surgical excision,aspiration or biopsy. The tissue may be fresh or frozen. In oneembodiment, the sample is fixed and embedded in paraffin or the like.The tissue sample may be fixed (i.e. preserved) by conventionalmethodology. One of ordinary skill in the art will appreciate that thechoice of a fixative is determined by the purpose for which the sampleis to be histologically stained or otherwise analyzed. One of ordinaryskill in the art will also appreciate that the length of fixationdepends upon the size of the tissue sample and the fixative used.

IHC may be performed in combination with additional techniques such asmorphological staining and/or fluorescence in-situ hybridization. Twogeneral methods of IHC are available; direct and indirect assays.According to the first assay, binding of antibody to the target antigen(e.g., EphB2) is determined directly. This direct assay uses a labeledreagent, such as a fluorescent tag or an enzyme-labeled primaryantibody, which can be visualized without further antibody interaction.In a typical indirect assay, unconjugated primary antibody binds to theantigen and then a labeled secondary antibody binds to the primaryantibody. Where the secondary antibody is conjugated to an enzymaticlabel, a chromogenic or fluorogenic substrate is added to providevisualization of the antigen. Signal amplification occurs becauseseveral secondary antibodies may react with different epitopes on theprimary antibody.

The primary and/or secondary antibody used for immunohistochemistrytypically will be labeled with a detectable moiety. Numerous labels areavailable which can be generally grouped into the following categories:

Aside from the sample preparation procedures discussed above, furthertreatment of the tissue section prior to, during or following IHC may bedesired, For example, epitope retrieval methods, such as heating thetissue sample in citrate buffer may be carried out (see, e.g., Leong etal. Appl. Immunohistochem. 4(3):201 (1996)).

Following an optional blocking step, the tissue section is exposed toprimary antibody for a sufficient period of time and under suitableconditions such that the primary antibody binds to the target proteinantigen in the tissue sample. Appropriate conditions for achieving thiscan be determined by routine experimentation. The extent of binding ofantibody to the sample is determined by using any one of the detectablelabels discussed above. Preferably, the label is an enzymatic label(e.g. HRPO) which catalyzes a chemical alteration of the chromogenicsubstrate such as 3,3′-diaminobenzidine chromogen. Preferably theenzymatic label is conjugated to antibody which binds specifically tothe primary antibody (e.g. the primary antibody is rabbit polyclonalantibody and secondary antibody is goat anti-rabbit antibody).

Specimens thus prepared may be mounted and coverslipped. Slideevaluation is then determined, e.g. using a microscope, and stainingintensity criteria, routinely used in the art, may be employed. Stainingintensity criteria may be evaluated as follows:

TABLE 2 Staining Pattern Score No staining is observed in cells. 0 Faint/barely perceptible staining is detected in more than 1+ 10% of thecells. Weak to moderate staining is observed in more than 10% of 2+ thecells. Moderate to strong staining is observed in more than 10% of 3+the cells.

Typically, a staining pattern score of about 2+ or higher in an IHCassay is diagnostic and/or prognostic. In some embodiments, a stainingpattern score of about 1+ or higher is diagnostic and/or prognostic. Inother embodiments, a staining pattern score of about 3 of higher isdiagnostic and/or prognostic. It is understood that when cells and/ortissue from a tumor or colon adenoma are examined using IHC, staining isgenerally determined or assessed in tumor cell and/or tissue (as opposedto stromal or surrounding tissue that may be present in the sample).

Other assay methods, known as competitive or sandwich assays, are wellestablished and widely used in the commercial diagnostics industry.

Competitive assays rely on the ability of a tracer EphB2 analogue tocompete with the test sample EphB2 for a limited number of anti-EphB2antibody antigen-binding sites. The anti-EphB2 antibody generally isinsolubilized before or after the competition and then the tracer andEphB2 bound to the anti-EphB2 antibody are separated from the unboundtracer and EphB2. This separation is accomplished by decanting (wherethe binding partner was preinsolubilized) or by centrifuging (where thebinding partner was precipitated after the competitive reaction). Theamount of test sample EphB2 is inversely proportional to the amount ofbound tracer as measured by the amount of marker substance.Dose-response curves with known amounts of EphB2 are prepared andcompared with the test results to quantitatively determine the amount ofEphB2 present in the test sample. These assays are called ELISA systemswhen enzymes are used as the detectable markers.

Another species of competitive assay, called a “homogeneous” assay, doesnot require a phase separation. Here, a conjugate of an enzyme with theEphB2 is prepared and used such that when anti-EphB2 antibody binds tothe EphB2 the presence of the anti-EphB2 antibody modifies the enzymeactivity. In this case, the EphB2 or its immunologically activefragments are conjugated with a bifunctional organic bridge to an enzymesuch as peroxidase. Conjugates are selected for use with anti-EphB2antibody so that binding of the anti-EphB2 antibody inhibits orpotentiates the enzyme activity of the label. This method per se iswidely practiced under the name of EMIT.

Steric conjugates are used in steric hindrance methods for homogeneousassay. These conjugates are synthesized by covalently linking alow-molecular-weight hapten to a small EphB2 fragment so that antibodyto hapten is substantially unable to bind the conjugate at the same timeas anti-EphB2 antibody. Under this assay procedure the EphB2 present inthe test sample will bind anti-EphB2 antibody, thereby allowinganti-hapten to bind the conjugate, resulting in a change in thecharacter of the conjugate hapten, e.g., a change in fluorescence whenthe hapten is a fluorophore.

Sandwich assays particularly are useful for the determination of EphB2or anti-EphB2 antibodies. In sequential sandwich assays an immobilizedanti-EphB2 antibody is used to adsorb test sample EphB2, the test sampleis removed as by washing, the bound EphB2 is used to adsorb a second,labeled anti-EphB2 antibody and bound material is then separated fromresidual tracer. The amount of bound tracer is directly proportional totest sample EphB2. In “simultaneous” sandwich assays the test sample isnot separated before adding the labeled anti-EphB2. A sequentialsandwich assay using an anti-EphB2 monoclonal antibody as one antibodyand a polyclonal anti-EphB2 antibody as the other is useful in testingsamples for EphB2.

The foregoing are merely exemplary detection assays for EphB2. Othermethods now or hereafter developed that use anti-EphB2 antibody for thedetermination of EphB2 are included within the scope hereof, includingthe bioassays described herein.

Articles of Manufacture

In another aspect of the invention, an article of manufacture containingmaterials useful for the treatment, prevention and/or diagnosis of thedisorders described above is provided. The article of manufacturecomprises a container and a label or package insert on or associatedwith the container. Suitable containers include, for example, bottles,vials, syringes, etc. The containers may be formed from a variety ofmaterials such as glass or plastic. The container holds a compositionwhich is by itself or when combined with another composition(s)effective for treating, preventing and/or diagnosing the condition andmay have a sterile access port (for example the container may be anintravenous solution bag or a vial having a stopper pierceable by ahypodermic injection needle). At least one active agent in thecomposition is an antibody of the invention. The label or package insertindicates that the composition is used for treating the condition ofchoice, such as cancer. Moreover, the article of manufacture maycomprise (a) a first container with a composition contained therein,wherein the composition comprises an antibody of the invention; and (b)a second container with a composition contained therein, wherein thecomposition comprises a further cytotoxic agent. The article ofmanufacture in this embodiment of the invention may further comprise apackage insert indicating that the first and second antibodycompositions can be used to treat a particular condition, e.g. cancer.Alternatively, or additionally, the article of manufacture may furthercomprise a second (or third) container comprising apharmaceutically-acceptable buffer, such as bacteriostatic water forinjection (BWFI), phosphate-buffered saline, Ringer's solution anddextrose solution. It may further include other materials desirable froma commercial and user standpoint, including other buffers, diluents,filters, needles, and syringes.

The following are examples of the methods and compositions of theinvention. It is understood that various other embodiments may bepracticed, given the general description provided above.

EXAMPLES

The following materials and methods were used in the Examples.Antibodies and Recombinant Proteins.

Monoclonal anti-phosphotyrosine conjugated with horseradish peroxidasewas obtained from Santa Cruz Biotechnology (Santa Cruz, Calif.).Antibodies to phospho-epidermal growth factor (EGF), EGF, phospho-p44/42MAP kinase, and p44/42 MAP kinase were purchased from Cell SignalingTechnology (Beverly, Mass.). Antibody to the GD epitope and the fusionproteins ephrin-B1-Fc and ephrin-B2-Fc were produced at Genentech (SouthSan Francisco, Calif.).

Cell Lines and Plasmids.

The human colon adenocarcinoma cell lines SW480, SW620, and Colo 205 andthe fibrosarcoma cell line HT1080 were obtained from the American TypeCulture Collection (Manassas, Va.). The HT1080-EphB2 and NT 1080-GD celllines were generated by cotransfection with a SV40-driven vectorencoding an NH2-terminal GD epitope-tagged form of EphB2 or emptyvector, respectively, and with a cytomegalovirus promoter-drivenpuromycin vector. Cells were selected in 1 μg/ml puromycin. TheSVT2-EphB2 cell line was established in the same fashion, except thatmouse 3T3 cells were cotransfected with a cytomegalovirus promotordriving Neo, and cells were selected in Geneticin (Life Technologies,Inc.) at 400 μg/ml. Cells were grown in high-glucose DMEM supplementedwith 10% fetal bovine serum, 2 mM glutamine, and penicillin-streptomycin(100 units/ml).

EphB2 ligand binding domain construct (ss.EphB2LBD.gD.GPI) was preparedby cloning a polynucleotide encoding amino acids 19 to 208 of humanEphB2 into a vector encoding a COOH-terminal GPI linker and anNH2-terminal GD epitope tag (ss.his.gD.GPI). This vector was transientlytransfected into 293 cells. Cells were grown in F12 DMEM Mix (50:50)media with 10% FBS. The transfected cells were subjected to furtheranalysis 48 hours following transfection.

RNA Expression Analysis.

For the analysis of tumor and normal colon tissue specimens (FIG. 3A),approximately 10 μg of total RNA from each human tumor or normal colontissue sample served as starting material for the preparation of probesrequired for oligonucleotide array analysis on the Affymetrix GeneChip.Probes were prepared according to the manufacturer's recommendations.After hybridization, the arrays were washed and stained withstreptavidin-phycoerythrin and then scanned with the Gene Array scanner(Agilent Technologies). Default parameters provided in the Affymetrixdata analysis software package were applied in determining the signalintensities, referred to as average differences. Sample normalizationwas done using global scaling as stated in the Affymetrix ExpressionAnalysis Technical Manual, and a target intensity of 1500 was used todetermine average difference expression values. For the analysis ofEphB2 mRNA expression in multiple human tumor and normal biopsy samples,the Affymetrix data were obtained from Gene Logic, Inc. (Gaithersburg,Md.). In the analysis shown, there are a total of 4841 samples (1808normal samples; 1545 cancer samples; and 1488 non-cancer diseasedsamples). Gene Logic data were also normalized using global scaling, butin this instance, the target intensity was 100. The Affymetrix data forEphB2 mRNA expression was generated from the U95 probe set ID 41678_at.Real-time PCR (TaqMan; Perkin-Elmer, Applied Biosystems) for EphB2 mRNAwas performed using gene-specific primers (5′-CGA-GCC-ACG-TTA-CAT-CA-3′(SEQ ID NO:10) and 5′-TCA-GTA-ACG-CCG-TTC-ACA-GC-3′ (SEQ ID NO:11)) andprobe (5′-CCC-ACA-CCC-AGT-ACA-CCT-TCG-AGA-TCC-3′ (SEQ ID NO:12)). For insitu hybridization, a 458-bp ³³P-labeled antisense riboprobe wasgenerated from an EphB2 PCR product using a primer with oligonucleotidesequence 5′-TCTGTCCATCTGTCCCGTCCT-3′ (SEQ ID NO:13) and a sense controlriboprobe with the primer 5′-GCCCTCCTGGTGCTCTATCC-3′ (SEQ ID NO:14).

Monoclonal Anti-EphB2 Antibodies.

BALB/c mice (Charles River Laboratories, Wilmington, Del.) wereimmunized with baculovirus-derived His8-tagged EphB2 receptor diluted inRibi adjuvant (Corixia, Hamilton, Mont.) twice a week, via footpad, fivedoses. B cells from lymph nodes were harvested from five micedemonstrating high serum titers and were fused with mouse myeloma cells(X63.Ag8.653; American Type Culture Collection). After 10-14 days, thesupernatants were screened for antibody production by direct ELISA andby flow cytometry on HT1080-GD and HT1080-EphBR cells. Positives weresubcloned twice to achieve monoclonality. For large-scale production ofpurified antibody, hybridoma cells were injected i.p. intopristine-primed BALB/c mice. The ascites fluids were pooled and purifiedby protein A affinity chromatography (Pharmacia Fast Protein LiquidChromatography; Pharmacia, Uppsala, Sweden).

Determination of 2H9Fv Sequences

Total RNA was extracted from hybridoma cells producing the mouse antihuman EphB2 monoclonal antibody 2H9, using RNeasy Mini Kit (Qiagen,Germany). The variable light (VL) and variable heavy (VH) domains wereamplified using RT-PCR with the following degenerate primers: Lightchain (LC) forward: 5′-GATCGATATCGTGATGACMCAGTCTCCATC-3′ (SEQ ID NO:15)

Light chain reverse: (SEQ ID NO:16) 5′-TTTDAKYTCCAGCTTGGTACC-3′ Heavychain (HC) forward: (SEQ ID NO:17)5′-GATCCGTACGCTCAGGTYCARCTSCAGCAGTCTGG-3′ Heavy chain reverse: (SEQ IDNO:17) 5′-ACAGTGGGCCCTTGGTGGAGGCTGMRGAGACDGTGASHRDRGT-3′

The forward primers were specific for the N-terminal amino acid sequenceof the VL and VH region. Respectively, the LC and HC reverse primerswere designed to anneal to a region in the constant light (CL) andconstant heavy domain 1 (CHI), which is highly conserved across species.Amplified VL was cloned into a pRK mammalian cell expression vector(Shields et al. J Biol Chem (2000) 276:659-604). Amplified VH wasinserted to a pRK mammalian cell expression vector. The polynucleotidesequence of the inserts was determined using routine sequencing methods.

Analysis of EphB2 Activation

The analysis of EphB2 activation by soluble Ephrin-Fc ligand wasperformed by stimulating the SVT2-EphB2 cell line with purifiedFc-EphrinB2 (5 μg/ml, 15 min) and detecting EphB2 autophosphorylationusing the following protocol. Cells were lysed inradioimmunoprecipitation assay buffer (50 mM Tris, 150 mM NaCl, 1%deoxycholate, 1% NP40, 2 mM sodium vanadate, 1 mM phenylmethylsulfonylfluoride, and complete proteinase inhibitor mixture (Roche MolecularBiochemicals)). Ten μg of anti-GD MAb were added to the lysates,followed by protein G-agarose (Life Technologies, Inc.), and incubatedovernight at 4° C. The immunoprecipitates were recovered, washed withlysis buffer, and subjected to SDS-PAGE and immunoblotting. Blots wereincubated with 1 μg/ml anti-phosphotyrosine mouse MAb conjugated withhorseradish peroxidase (Santa Cruz Biotechnology) or anti-GD mouse MAb.Goat antimouse horseradish peroxidase was used as a secondary antibody,and the blots were washed and developed using the EnhancedChemiluminescence system (Pierce). Analysis of MAP kinase activation wascarried out using the HT1080-EphB2 cell line. Cells were serum starvedfor 12 h and either left untreated or stimulated with EGF 100 ng/ml inthe absence or presence of 5 μg human Fc-EphrinB2/ml. Cell lysates wereequalized for protein concentration, subjected to SDS-PAGE, andimmunoblotted with anti-phospho-EGF receptor or phospho-MAP kinaseantibody.

Flow Cytometry

For flow cytometry, cells were grown to 90% confluence and removed fromplates using Cell Dissociation Buffer (Invitrogen). Cells were washedand resuspended in fluorescence-activated cell-sorting buffer (PBS with1% BSA) and incubated for 45 min with anti-EphB2 MAb 2H9 or anti-GDantibody (Genentech) followed by 30-min incubation with antimousesecondary antibody conjugated to phycoerythrin. Analysis was performedon FACSscan.

Binding Affinity, ELISA, and Isotype Testing

Binding affinity of Mab 2H9 was determined by surface plasmon resonanceusing Pharmacia BIAcore® 3000 (BIAcore AB, Uppsala, Sweden) at roomtemperature (see, e.g., Morton et al. (1998) Methods in Enzymology, 295,268-294). Anti-EphB2 antibodies were immobilized to the sensor chip(CM5) through primary amine groups. The carboxymethylated sensor chipsurface matrix was activated by injecting 20 μl of a mixture of 0.025 MN-hydroxysuccinimide and 0.1 M N-ethyl-N′(dimethylaminopropyl)carbodiimide at 5 μl/min. 5-10 μl of 10 μg/ml solution of anti-EphB2antibodies in 10 mM sodium acetate, pH 4.5, were injected at 5 μl/min.After coupling, unoccupied sites on the chip were blocked by injecting20 μl of 1M ethanolamine, pH 8.5. The running buffer was PBS containing0.05% polysorbate 20. For kinetic measurements, two-fold serialdilutions of polyhis-tagged EphB2 in running buffer were injected overthe flow cells for 3 minutes at a flow rate of 30 μl/min and the boundpolyhis tagged EphB2 was allow to dissociate for 20 minutes. The bindingsurface was regenerated by injecting 20 μl of 10 mM glycine-HCl (pH1.5). Flow cell one, which was activated but did not have antibodyimmobilized, was used as a reference cell. There was no significantnon-specific binding of polyhis tagged EphB2 to flow cell one. Forcalculate apparent binding affinity, data were analyzed using a 1:1binding model using global fitting. The association and dissociationrate constants were fitted simultaneously (BIAevaluation software).

Mab 2H9 was determined to bind human and mouse EphB2 polypeptide usingELISA according to the following protocol. Microtiter plates (Nunc,Roskilde, Sweden), were coated with 100 μl/well of baculovirus-derivedHis8-tagged EphB2 receptor at 1 μg/ml in 0.05 M carbonate buffer, pH9.6, overnight at 4° C. Plates were washed with PBS/0.05% T20 andblocked with PBS bovine serum albumin (BSA)/T20. Hybridoma supernatantswere added (100 μl/well), incubated for 1 h at room temperature withagitation. Following the wash step, bound antibodies was detected withgoat anti-mouse IgG (Fc specific) peroxidase conjugate (Sigma, St.Louis, Mo.; diluted 1:10 K in PBS/BSA/T20 buffer; incubated for 1 h atRT). The plates were developed with TMB substrate solution(KPL/Kirkegaard & Perry Laboratories, Galthersburg, Md.) and reactionwas stopped with TMB 1-component stop solution (KPL). Plates were readat absorbance of 450 nm, with reference at 630 nm using an automatedplate reader.

Reactivity of Mab 2H9 with related Eph receptor EphB3 was tested asfollows. 293 cells expressing EphB3 were generated by transienttransfection with a vector containing EphB3 ECD sequences, anNH2-terminal GD tag and a COOH-terminal GPI linker. After 48 hours, Mab2H9 was incubated with the cells, then, following washing, the cell weresubjected to FACS analysis as described above. Mab 2H9 showed very lowcross-binding with EphB3.

Mab 2H9 was determined to be isotype IgG1, as determined using standardmethods.

Antibody Binding and Internalization, Immunohistochemistry.

Purified MAb 2H9 was iodinated using the lactoperoxidase method, and theradiolabeled antibody was purified from free ¹²⁵I-Na by gel filtrationchromatography using a Pharmacia PD-10 column. Assessment ofinternalization was carried out essentially as described previously(Gladhaug I. P. et al., J. Biol. Chem., 263: 12199-12203, 1988). Cellswere incubated with iodinated antibody on ice and then shifted to 37° C.for 4 h, followed by an acid/salt/urea incubation at 4° C. to dissociatesurface-bound ligand. Total surface-bound and internalized antibody wasdetermined by scintillation counting. Internalization of EphB2 was alsoassessed by immunofluorescence staining of cells.

Immunohistochemical staining of human colon tumor sections withanti-EphB2 antibody was performed on frozen tissue sections. Sectionscontaining malignant epithelial cells of a colorectal adenocarcinomawere incubated with primary antibody 2H9 at a concentration of 5 μg/ml,followed a biotinylated horse antimouse IgG affinity-purified antiserum.As control, an adjacent section was incubated with an irrelevant primaryantibody and counterstained with hematoxylin.

Slides containing HT1080-EphB2 cells were incubated with 1 μg/ml 2H9antibody for 30 min on ice and then shifted to 37° C. in a CO2 incubatorfor 1 h. The slides were washed in PBS, fixed in 3% paraformaldehyde,and incubated with rhodamine-conjugated antimouse IgG antibody (JacksonImmunoresearch Laboratories) at a 1:200 dilution for 20 min at roomtemperature. The number of cell surface MAb 2H9 binding sites wasestimated by incubating cells for 4 h on ice with a fixed concentrationof ¹²⁵I-labeled MAb 2H9 combined with increasing concentrations ofunlabeled MAb 2H9, essentially as described previously (Holmes W. etal., Science, 256: 1205-1210, 1992).

Determination of EphB2 Ligand Binding Domain and Mapping of 2H9 BindingDeterminant

To determine EphB2's ligand binding domain, 48 hours following transienttransfection, 1 μl EphB2 ligand (ephrinB1-IgG at 91 ng/μl) was added toss.EphB2LBD.gD.GPI-293 cells, and cells were kept on ice for 20 minutes.Following two washes, cells were incubated with FITC-conjugated Fcspecific anti-human IgG antibody (Sigma catalog no. F9512) on ice for 30minutes. Following two more washed, cells were subjected to FACSanalysis as described above. The results demonstrated that EphB2 ligandEphrinB1 bound EphB2 amino acids 19-208, thus defining EphB2 amino acids19-208 as containing the EphB2 ligand binding domain. No binding wasobserved using cells that expressed a control vector.

To determine reactivity of Mab 2H9 with amino acid numbers 19-208 ofEphB2, Mab 2H9 (1 μg/ml) or anti-GD antibody (4 μg/ml) were incubatedwith ss.EphB2LBD.gD.GPI-293 cells, then, following washing, cells weresubjected to FACS analysis as described above. The results demonstratedthat GD protein and EphB2 ligand binding domain protein was detected bythese antibodies. These results indicated that Mab 2H9 bound the EphB2ligand binding domain. No 2H9 or anti-GD antibody binding was observedusing cells that expressed a control vector.

Preparation of Anti EphB2 Mab 2H9 Immunoconjugates

The conjugation of the anti-EphB2 antibody 2H9 and controlanti-interleukin (IL)-8 antibody with MC-vc-PAB-MMAE and the conjugationof 2H9 with MC-vc-PAB-MMAF were performed as described elsewhere(Doronina S. O. et al. Nat. Biotechnol., 21: 778-784, 2003; U.S. Ser.No. 10/983,340, filed Nov. 5, 2004). The conjugation of 2H9 with MC-MMAEand MC-MMAF was performed as described in U.S. Ser. No. 10/983,340,filed Nov. 5, 2004, following the protocol provided in Doronina, supra.The conjugation of 2H9 with SMCC-DM1 and SPP-DM1 was performed asdescribed in U.S. Ser. No. 10/960,602, filed Oct. 8, 2004.

In Vitro Tumor Cell Killing Assays.

The HT1080-EphB2 cell line or the vector control cell line were added toeach well of 96-well microtiter plates at 1.5×10³ cells/well, 100μl/well, and incubated overnight at 37° C. in a humidified atmosphere of5% CO2. Cells were exposed to various concentrations of MAb2H9-MC-vc-PAB-MMAE or Mab anti-IL-8-MC-vc-PAB-MMAE based on 1:3 serialdilutions. After incubation for 48 h, Cell Titer-Glo reagent (Promega,Madison, Wis.) was added to the wells at 100 μl/well, and after a 10-minincubation at room temperature, the luminescent signal was recorded.

In a separate experiment, HT1080-EphB2 cells were exposed to variousconcentrations of 2H9-SPP-Dm1, 2H9-SMCC-DM1, 2H9-MC-vc-PAB-MMAE,2H9-MC-vc-PAB-MMAF or anti-interleukin-8-MC-vc-PAB-MMAE, essentially asdescribed above, and cell viability was measured after 2 days asdescribed above.

In Vivo Tumor Growth Assays.

Female nude mice (Charles River Laboratories, Hollister, Calif.) weremaintained in accordance with the guide for the care and use oflaboratory animals. HT1080-EphB2 and HT1080-GD cells were harvested,resuspended in PBS, and injected s.c. into the right and left flanks(1×10⁶ cells/flank), respectively, of 6-8-week-old mice. When tumorsreached approximately 100 mm³, animals were dosed i.p. with 0.2 ml ofnative EphB2 MAb or 2H9-MC-vc-PAB-MMAE or Mab anti-IL-8-MC-vc-PAB-MMAEonce a week i.v. at a final dose of 3 mg/kg body weight. The tumorvolumes were determined by measuring the length (l) and width (w) andcalculating the volume (V=lw2/2) as described previously.

Assays with the CXF1103 tumor line were performed by Oncotest Gmbh(Feiburg, Germany). See U.S. Pat. No. 6,271,342. Affymetrixoligonucleotide array analysis was performed on tumors from the Oncotestcollection, which demonstrated expression of EphB2 mRNA in CXF1103. Thiswas confirmed by real-time PCR and immunohistochemistry. CXF 1103 is ahuman colon tumor established by serial passage in nude mice. Groups of10 nude mice of NMRI background received s.c. tumor implants to obtain30 mice bearing tumors of similar sizes for randomization. Tumors weregrown to an average size of 100-200 mg, whereupon treatment with vehiclecontrol, control antibody conjugate anti-GD-MC-vc-PAB-MMAE, oranti-EphB2 antibody conjugate 2H9-MC-vc-PAB-MMAE was initiated by i.v.injection. Antibody conjugates were administered at 3 mg/kg body weightat 7-day intervals for 3 weeks.

Results Example 1 Analysis of E1hB2 mRNA and Protein Expression inCancer and Normal Human Tissues

EphB2 mRNA and protein are overexpressed in cancer tissues.Oligonucleotide-based microarray expression analysis was performed on 38human colorectal tumors and 7 normal colon biopsy samples. Data miningrevealed that EphB2 was overexpressed by 2-6-fold in the majority of thetumors relative to the average expression level of the normal samples(FIG. 3A). To confirm the overexpression in colon cancers, real-time PCR(TaqMan) was performed on 11 additional human colorectal tumors, eachreferenced to a patient-matched normal colon sample. These data werehighly consistent with the microarray data (FIG. 3B). On mining of alarger database, containing microarray data from over 4800 human biopsysamples, it was noted that EphB2 mRNA was preferentially expressed inintestinal tissue, with increased expression in colorectal, soft tissuecancers (such as fibrosarcoma and other sarcomas), and gastric cancersrelative to numerous other tissues.

EphB2 mRNA expression was also examined by in situ hybridization ontissue microarrays. By this method, the only normal human tissues inwhich EphB2 protein expression was detected were the colon and smallintestine. In situ hybridization was also carried out on agastrointestinal tissue microarray containing samples from a variety ofcancers. Here, EphB2 mRNA expression was seen in 12 of 18 primarycolonic adenocarcinomas, 6 of 8 metastatic adenocarcinomas to the liver,2 of 9 primary gastric carcinomas, and 1 of 4 esophageal carcinomas. Noexpression was observed in four of four pancreatic adenocarcinomas.Examples of expression in normal colonic mucosa and colorectal cancer byin situ hybridization are shown FIG. 4A.

Mab 2H9 reacted strongly with tissue sections obtained from human colonadenocarcinomas (FIG. 4B). EphB2 protein expression has beendemonstrated at all stages of colorectal tumorigenesis, including allnormal crypts, and overexpression in 77% of adenomas, 82% of primarycancers, and 64% of metastases. See co-pending co-owned U.S. PatentApplication No. 60/642,164, filed Jan. 6, 2005.

Example 2 Preparation and Characterization of Anti-EphB2 MonoclonalAntibody 2H9

Antibodies to the extracellular sequence of EphB2 were prepared asdescribed above, and several hybridomas were cloned that expressed MAbsreactive with the purified EphB2 immunogen and with the full-lengthEphB2 by flow cytometry (fluorescence-activated cell sorting) of cellsexpressing EphB2. MAbs from positive hybridomas were purified andcompared for reactivity against colorectal cancer cell lines thatendogenously express EphB2 and against cell lines engineered tooverexpress the receptor (HT-1080EphB2 and SVT2EphB2). A MAb designated2H9 performed well in these assays.

Elisa analysis demonstrated that Mab 2H9 bound human and mouse EphB2.Isotype analysis revealed that Mab 2H9 possessed an IgG1 isotype. Mab2H9 binding affinity was also determined by BiaCore analysis. Mab 2H9bound human EphB2 with K_(a) (1/Ms) of 8.28E+04, K_(d) (1/s) of1.03E-05, and Kd (nM) of 0.12. Mab 2H9 showed very low cross-reactivitywith related Eph receptor, EphB3, in a FACS-based analysis.

Example 3 Mab 2H9 Inhibits EphB2 Activation by Competitively InhibitingEphB2 Ligand Binding

The tyrosine kinase activity of EphB2 can be activated on binding of thereceptor with ephrinB ligands (Davis S. et al. Science, 266: 816-819,1994). This was observed when the murine 3T3 cell line expressing humanEphB2 was incubated with a purified Fc-ephrinB2 fusion protein (FIG.5A). MAb 2H9 was tested in this assay. The tyrosine autophosphorylationof EphB2 by Fc-ephrinB2 was inhibited when the cells were preincubatedwith MAb 2H9, whereas a control antibody had no effect (FIG. 5A). Themechanism by which MAb 2H9 inhibits EphB2 activation was investigatedand found to involve competitive inhibition of ligand binding. This wasdetermined by performing flow cytometry on cells incubated with theFc-ephrinB1 ligand after their incubation with or without MAb 2H9. Inthis experiment, a positive fluorescence-activated cell-sorting signalresults from the specific binding of FITC-conjugated antihuman Fcantibody to the bound Fc-ephrinB1 ligand. Increasing amounts of MAb 2H9resulted in a corresponding decrease in Fc-ephrinB1 ligand binding (FIG.5B). The loss of binding was not due to antibody-mediated receptoruptake because all incubations were performed on ice, where receptorinternalization is minimal. Thus, MAb 2H9 inhibited the binding ofephrin ligands to the EphB2 receptor.

To determine whether MAb 2H9 was able to affect the mitogenic ortumorigenic potential of cancer cells, growth effects of Mab 2H9 onvarious cell lines in vitro was determined. However, MAb 2H9 did notexhibit any specific effect on the growth of various cell lines in vitrothat express the receptor (cell lines HT-1080-EphB2 and PC3-EphB2). Aninhibition of cell growth might not be expected, however, because Ephreceptors are not considered to be mitogenic and have even been reportedto interfere with mitogenic signaling as assessed by the activity of theMAP kinase pathway (Kim et al., FASEB J., 16: 1126-1128, 2002; Elowe etal., Mol. Cell. Biol., 21: 7429-7441, 2001). To assess this in atumorigenic cell line strongly responsive to EGF, stable clones of thefibrosarcoma cell line HT1080 overexpressing EphB2 (HT1080-EphB2) weregenerated. The HT1080 cell line produced ephrinB1 transcript. EphrinB2did not inhibit activation of the MAP kinase pathway by EGF in thesecells but rather appeared to enhance it slightly.

Example 4 Mab 2H9 is Internalized After Binding EphB2

Internalization of MAb 2H9 after EphB2 binding was investigated.HT1080-EphB2 cells were incubated with MAb 2H9 on ice for 30 minutes andthen shifted to 37° C. for 1 hour before fixation and staining withsecondary antibody. Compared with cells kept on ice for the course ofthe experiment, the cells shifted to 37° C. contained significantamounts of internalized antibody (FIG. 6A). MAb 2H9 uptake was examinedby incubating cells with ¹²⁵I-radiolabeled antibody at 4° C. The amountof ¹²⁵I-labeled MAb 2H9 that was internalized after cells were shiftedto 37° C. for 1 hour was approximately double that of cells maintainedat 4° C. (FIG. 6B). MAb 2H9 was readily internalized on binding toEphB2. Thus, Mab 2H9 is suitable for immunoconjugate therapy approacheswherein the uptake or internalization of the antigen-antibody complexresults in preferential release of drug inside of the cancer cells.

Example 5 Mab 2H9 Binds to the EphB2 Ligand Binding Domain

The EphB2 ligand binding domain was defined by incubatingss.EphB2LBD.gD.GPI-293 cells with EphrinB1-IgG, then subjecting thecells to FACS analysis. The results demonstrated that an EphB2 ligand,EphrinB1, bound EphB2 amino acids 19-208, thus defining EphB2 aminoacids 19-208 (FIG. 11) as containing the EphB2 ligand binding domain. Nobinding was observed using cells that expressed a control vector.

Mab 2H9 binding to the EphB2 ligand binding domain was investigated byincubating Mab 2H9 or anti-GD antibody with ss.EphB2LBD.gD.GPI-293cells, then subjecting the cells to FACS analysis. The resultdemonstrated that GD protein and EphB2 ligand binding domain wasdetected by these antibodies, indicating that Mab 2H9 bound the EphB2ligand binding domain. No 2H9 or anti-GD antibody binding was observedusing cells that expressed a control vector.

Example 6 Mab 2H9 Immunoconjugate Effectively Kills Tumor Cells in vitro

MAb 2H9 was covalently coupled to the drug MMAE through the linkerMC-vc-PAB that is susceptible to cleavage by cathepsin B (Weiner L. M.Semin. Oncol., 26: 43-51, 1999). On cleavage by cathepsin B, active MMAEis released, disrupting the dynamics of tubulin polymerization in thecell. The 2H9-MC-vc-PAB antibody drug conjugate (immunoconjugate) wastested in vitro by treating the HT1080 cancer cells with increasingconcentrations of antibody. Both the vector control HT1080 cell line(HT1080-GD) and the clonal derivative overexpressing EphB2(HT1080-EphB2) were killed by 2H9-MC-vc-PAB-MMAE at significantly lowerconcentrations relative to control antibody conjugateanti-IL-8-MC-vc-PAB (FIG. 7). No effect was seen with underivatized MAb2H9 up to a concentration of 10 mg/ml. The antibody concentrationrequired for half-maximal cell killing (IC50) was 0.006 μg/ml for cancercells HT1080-EphB2.

To relate cell killing to receptor copy number, quantitative bindingassays were performed using MAb 2H9 on the HT1080-GD and HT1080-EphB2cell lines. By Scatchard analysis, approximately 71,000 and 308,000copies/cell for these two lines, respectively, were estimated (FIG. 8A).For both cell lines, the apparent dissociation constant for MAb 2H9 wasapproximately 4 nM. The difference in EphB2 copy number was also evidentfrom the relative fluorescence intensity observed when flow cytometrywas performed with MAb 2H9 on the two cell lines (FIG. 8B). Also, theconjugation of MAb 2H9 with MC-vc-PAB-MMAE did not appreciably affectits binding properties to the HT1080 cells. The relative difference inreceptor copy number on the two HT1080 cell lines was again evident fromthe binding of 2H9-MC-vc-PAB-MMAE (FIG. 8C). These results indicatedthat target copy number is an important factor in determining theefficacy of a drug-conjugated antibody. In the case of EphB2, a moderatedifference in copy number resulted in a much greater difference in theIC50 values determined in vitro.

In a separate experiment, HT1080-EphB2 cells were exposed to variousconcentrations of 2H9-SPP-Dm1, 2H9-SMCC-DM1, 2H9-MC-vc-PAB-MMAE,2H9-MC-vc-PAB-MMAF or anti-interleukin-8-MC-vc-PAB-MMAE essentially asdescribed above, and cell viability was measured after 2 days asdescribed above. HT1080-EphB2 cells were killed by 2H9-MC-vc-PAB-MMAE,2H9-SMCC-DM1 and 2H9-SPP-DM1 at significantly lower concentrationsrelative to control antibody conjugate anti-IL-8-MC-vc-PAB-MMAE (FIG.9A). Ht1080-EphB2 cells were killed by 2H9-MC-vc-PAB,2H9-MC-vc-PAB-MMAF, 2H9-SPP-DM1 and 2H9-SMCC-DM1 (FIG. 9B).

Example 7 Mab 2H9 Antibody Drug Conjugate Effectively Kills Tumor Cellsin vivo

2H9-MC-vc-PAB-MMAE was tested for in vivo efficacy by administration tonude mice bearing human tumor xenografts. Tumors were established byinoculating mice on one flank with the HT1080-GD cells and on theopposite flank with HT1080-EphB2 cells. Tumors were grown to a size of100-200 mm³ before i.v. administration of 2H9-MC-vc-PAB-MMAE once perweek at a dose of 3 mg/kg. Additional animals were treated with vehiclecontrol or with control antibody anti-IL-8-MC-vc-PAB-MMAE at 3 mg/kg. Inthis experiment, the HT1080-EphB2 cell line grew more rapidly than theHT1080-GD vector control cell line under control conditions. It is notbelieved that this is due to overexpression of EphB2 because previoustesting of HT1080-EphB2 clones did not reveal a reproducible effect ontumor growth rate. Nevertheless, both types of tumors responded well totreatment with 2H9-MC-vc-PAB-MMAE relative to vehicle control andcontrol antibody conjugate anti-IL-8-MC-vc-PAB-MMAE (FIG. 10A). Controlanimal groups were terminated between day 7 and 14 due to the aggressivegrowth of their tumors. Animals treated with 2H9-MC-vc-PAB-MMAE weremaintained out to 4 weeks, when treatment was discontinued. By contrast,naked Mab 2H9 antibody was tested in a by growing the HT1080-EphB2 cellline as a tumor xenograft in nude mice that were then given MAb 2H9 at adose of 10 mg/kg body weight twice per week. However, treatment withnaked MAb 2H9 did not result in any significant effect on the rate oftumor growth in this assay.

As an additional test of in vivo efficacy, a human colon tumorestablished by serial passage in nude mice was implanted s.c., andgrowth was measured during a treatment course identical to thatdescribed for the HT1080 model above. Significant growth retardation wasagain observed with 2H9-MC-vc-PAB-MMAE, relative to vehicle control orcontrol antibody anti-GD-MC-vc-PAB-MMAE (FIG. 10B). Overall, theseresults demonstrated specificity and efficacy of 2H9-MC-vc-PAB-MMAE inin vivo tumor growth models.

The following hybridoma has been deposited with the American TypeCulture Collection, PO Box 1549, Manassas, Va., 20108, USA (ATCC):

Cell Lines ATCC Accession No. Deposit Date Hybridoma 2H9.11.14 PTA-6606Feb. 24, 2005

These deposits were made under the provisions of the Budapest Treaty onthe International Recognition of the Deposit of Microorganisms for thePurpose of Patent Procedure and the Regulations thereunder (BudapestTreaty). This assures maintenance of a viable deposit for 30 years fromthe date of deposit. These cell lines will be made available by ATCCunder the terms of the Budapest Treaty, and subject to an agreementbetween Genentech, Inc. and ATCC, which assures permanent andunrestricted availability of the cell lines to the public upon issuanceof the pertinent U.S. patent or upon laying open to the public of anyU.S. or foreign patent application, whichever comes first, and assuresavailability of the cell lines to one determined by the U.S.Commissioner of Patents and Trademarks to be entitled thereto accordingto 35 USC §122 and the Commissioner's rules pursuant thereto (including37 CFR §1.14 with particular reference to 886 OG 638).

The assignee of the present application has agreed that if the depositedcell lines should be lost or destroyed when cultivated under suitableconditions, they will be promptly replaced on notification with aspecimen of the same cell line. Availability of the deposited cell linesis not to be construed as a license to practice the invention incontravention of the rights granted under the authority of anygovernment in accordance with its patent laws.

Although the foregoing invention has been described in some detail byway of illustration and example for purposes of clarity ofunderstanding, the descriptions and examples should not be construed aslimiting the scope of the invention.

1. An anti-EphB2 antibody comprising: at least one, two, three, four,five, and/or six hypervariable region (HVR) sequences selected from thegroup consisting of: (a) HVR-L1 comprising sequence KSSQSLLNSGNQENYLA(SEQ ID NO:1); (b) HVR-L2 comprising sequence GASTRES (SEQ ID NO:2); (c)HVR-L3 comprising sequence QNDHSYPFT (SEQ ID NO:3); (d) HVR-H1comprising sequence SYWMH (SEQ ID NO:4); (e) HVR-H2 comprising sequenceFINPSTGYTDYNQKFKD (SEQ ID NO:5); and (f) HVR-H3 comprising sequenceRLKLLRYAMDY (SEQ ID NO:6), wherein the antibody specifically binds humanEphB2.
 2. The anti-EphB2 antibody of claim 1, wherein the antibody ofthe invention comprises a light chain comprising at least one, at leasttwo, or all three of HVR sequences selected from the group consisting ofKSSQSLLNSGNQENYLA (SEQ ID NO:1), GASTRES (SEQ ID NO:2), and QNDHSYPFT(SEQ ID NO:3).
 3. The anti-EphB2 antibody of claims 1 or 2, wherein theantibody comprises a heavy chain comprising at least one, at least twoor all three of HVR sequences selected from the group consisting ofSYWMH (SEQ ID NO:4), FINPSTGYTDYNQKFKD (SEQ ID NO:5), and RLKLLRYAMDY(SEQ ID NO:6).
 4. The anti-EphB2 antibody of claim 1, wherein theantibody comprises (a) a heavy chain comprising at least one, at leasttwo or all three of HVR sequences selected from the group consisting ofSYWMH (SEQ ID NO:4), FINPSTGYTDYNQKFKD (SEQ ID NO:5), and RLKLLRYAMDY(SEQ ID NO:6); and (b) a light chain comprising at least one, at leasttwo or all three of CDR sequences selected from the group consisting ofKSSQSLLNSGNQENYLA (SEQ ID NO:1), GASTRES (SEQ ID NO:2), and QNDHSYPFT(SEQ ID NO:3).
 5. The anti-EphB2 antibody of claim 1, wherein theantibody comprises a light chain variable domain having the sequence:(SEQ ID NO:7) DIVMTQSPSSLSVSAGEKVTMNCKSSQSLLNSGNQENYLAWYQQKPGQPPKLLIYGASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCQNDHSY PFTFGAGTKVEIKR.


6. The anti-EphB2 antibody of claim 1 or 5, wherein the antibodycomprises a heavy chain variable domain having the sequence: (SEQ IDNO:8) QVQLQQSGAELAKPGASVKMSCKASGYTFTSYWMHWVKQRPGQGLEWIGFINPSTGYTDYNQKFKDKATLTVKSSNTAYMQLSRLTSEDSAVYYCTRRLK LLRYAMDYWGQGTTLTVSA.


7. An isolated antibody comprising at least one hypervariable sequencecomprising a sequence selected from the group consisting of HVR-L1,HVR-L2, HVR-L3, HVR-H1, HVR-H2, and HVR-H3 of the antibody produced byhybridoma cell line having American Tissue Type Culture (ATCC) No.PTA-6606, wherein said isolated antibody specifically binds human EphB2.8. An isolated antibody comprising heavy and/or light chain variabledomain of the antibody produced by hybridoma cell line having AmericanTissue Type Culture (ATCC) No. PTA-6606, wherein said isolated antibodyspecifically binds human EphB2.
 9. An isolated antibody that binds to asame epitope on human EphB2 as the antibody produced by hybridoma cellline having American Tissue Type Culture (ATCC) No. PTA-6606.
 10. Anisolated antibody that competes with an antibody produced by hybridomacell line having American Tissue Type Culture (ATCC) No. PTA-6606 forbinding to human EphB2.
 11. An isolated antibody encoded by antibodycoding sequences of hybridoma cell line having American Tissue TypeCulture (ATCC) No. PTA-6606
 12. The antibody of any of claims 1-11,wherein the antibody is a monoclonal antibody.
 13. The antibody of anyof claims 1-12, wherein the antibody is selected from the groupconsisting of a chimeric antibody, a humanized antibody, an affinitymatured antibody, a human antibody, and a bispecific antibody.
 14. Theantibody of any of claims 1-12, wherein the antibody is an antibodyfragment.
 15. The antibody of any of claims 1-14, wherein the antibodyis conjugated to a growth inhibitory agent.
 16. The antibody of any ofclaims 1-14, wherein the antibody is conjugated to a cytotoxic agent.17. The antibody of claim 16, wherein the cytotoxic agent is selectedfrom the group consisting of toxins, antibiotics, radioactive isotopesand nucleolytic enzymes.
 18. The antibody of any of claims 1-14, whereinthe antibody is conjugated to an agent selected from the groupconsisting of a maytansinoid, an auristatin, a dolastatin, and acalicheamicin.
 19. The antibody of claim 18, wherein the agent isselected from the group consisting of DM1, DM3, DM4, MMAE, and MMAF. 20.A polynucleotide encoding an antibody of any of claims 1-14.
 21. Avector comprising the polynucleotide of claim
 20. 22. The vector ofclaim 21, wherein the vector is an expression vector.
 23. A host cellcomprising a vector of claim 21 or
 22. 24. The host cell of claim 23,wherein the host cell is prokaryotic.
 25. The host cell of claim 23,wherein the host cell is eukaryotic.
 26. The host cell of claim 25,wherein the host cell is mammalian.
 27. A method for making ananti-EphB2 antibody, said method comprising (a) expressing a vector ofclaim 22 in a suitable host cell, and (b) recovering the antibody.
 28. Amethod for making an anti-EphB2 immunoconjugate, said method comprising(a) expressing a vector of claim 22 in a suitable host cell, and (b)recovering the antibody.
 29. The method of claim 27 or 28, wherein thehost cell is prokaryotic.
 30. The method of claim 27 or 28, wherein thehost cell is eukaryotic.
 31. A method for treating or preventing atumor, a cancer, or a cell proliferative disorder associated withincreased expression or activity of EphB2, the method comprisingadministering an effective amount of the anti-EphB2 antibody of any ofclaims 1-19 to a subject in need of such treatment.
 32. The method ofclaim 31, wherein the cancer is selected from the group consisting ofsmall cell lung cancer, neuroblastomas, melanoma, breast carcinoma,gastric cancer, colorectal cancer, and hepatocellular carcinoma.
 33. Themethod of claim 32, wherein the cancer is colorectal cancer.
 34. Amethod for killing a cancer or tumor cell, the method comprisingadministering an effective amount of an anti-EphB2 antibody of any ofclaims 15-19 to a subject in need of such treatment.
 35. The method ofclaim 34, wherein the cancer or tumor cell is a colon cancer cell or agastric cancer cell.
 36. A method for detection of FGF19, the methodcomprising detecting FGF19-anti-FGF19 antibody complex in a biologicalsample.
 37. A method for diagnosing a disorder associated with FGF19expression, the method comprising detecting FGF19-anti-FGF19 antibodycomplex in a biological sample from a patient having or suspected ofhaving the disorder.
 38. The method of claim 37, wherein the disorder isa tumor, cancer, and/or a cell proliferative disorder.
 39. The method ofany of claims 36-38, wherein the anti-FGF19 antibody is detectablylabeled.
 40. A composition comprising an anti-FGF19 antibody of any ofclaims 1-19.
 41. A composition comprising a polynucleotide of any ofclaims 20-22.
 42. The composition of claim 40 or 41, wherein thecomposition further comprises a carrier.